Difference between revisions of "User:Jarle Pahr"

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==Notes==
 
==Notes==
  
===0-9===
 
  
[[User:Jarle Pahr/13C|13C]]
+
See [[User:Jarle Pahr/Notes|Notes]]
  
[[User:Jarle Pahr/16S_RNA|16S RNA]]
+
==Projects==
  
===A===
+
[[User:Jarle Pahr/Notebook/ppGpp Msc|ppGpp MSc. project]]
  
[[User:Jarle Pahr/Algae|Algae]]
+
==Organisms==
  
[[User:Jarle Pahr/Alginate|Alginate]]
 
  
[[User:Jarle Pahr/Algorithms|Algorithms]]
+
See [[User:Jarle Pahr/Organisms|Organisms]]
  
[[User:Jarle Pahr/Allpaths|Allpaths]]
+
==Interesting articles==
 +
[http://www.ncbi.nlm.nih.gov/pubmed/21847113 Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen]
  
[[User:Jarle Pahr/Android|Android]]
+
[http://www.ncbi.nlm.nih.gov/pubmed/16330045 Environmentally controlled invasion of cancer cells by engineered bacteria]
  
[[User:Jarle Pahr/Annotation|Annotation]]
+
[http://www.ncbi.nlm.nih.gov/pubmed/18263722 Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli]
  
[[User:Jarle Pahr/Articles|Articles]]
+
[http://www.cell.com/abstract/S0092-8674%2812%2900776-3 A Whole-Cell Computational Model Predicts Phenotype from Genotype]
  
[[User:Jarle Pahr/Article_reviews|Article reviews]]
+
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11516.html Genetic programs constructed from layered logic gates in single cells]
  
[[User:Jarle Pahr/Automation|Automation]]
+
==Research centres/labs==
  
[[User:Jarle Pahr/Applications|Apps]]
+
Wyss institute: http://wyss.harvard.edu/
  
[[User:Jarle Pahr/Alignment|Alignment]]
+
Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/
  
[[User:Jarle Pahr/Arduino|Arduino]]
+
Cold Spring Harbor Laboratory: http://www.cshl.edu/
  
[[User:Jarle Pahr/Assembly|Assembly]]
+
Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/
  
[[User:Jarle Pahr/Annotation|Annotation]]
+
Insititute for Systems Biology: https://www.systemsbiology.org
  
[[User:Jarle Pahr/Antibiotics|Antibiotics]]
+
Virginia Bioinformatics Institute: https://www.vbi.vt.edu/
  
[[User:Jarle Pahr/AWS|AWS]]
+
European Bioinformatics Institute: http://www.ebi.ac.uk/
  
===B===
+
ATCC: http://www.lgcstandards-atcc.org/
  
[[User:Jarle Pahr/BAM|BAM]]
+
European Molecular Biology Laboratory (EMBL): http://www.embl.de/
  
[[User:Jarle Pahr/Bedtools|Bedtools]]
+
http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html
  
[[User:Jarle Pahr/Beer|Beer]]
 
  
[[User:Jarle Pahr/BGI|BGI]]
+
http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
  
[[User:Jarle Pahr/Bibliometry|Bibliometry]]
+
http://korflab.ucdavis.edu/
  
[[User:Jarle Pahr/Biohacking|Biohacking]]
+
==Research programs/projects==
  
[[User:Jarle Pahr/Biology|Biology]]
+
Statseq: http://www2.ab.wur.nl/statseq/
  
[[User:Jarle Pahr/Biosensors|Biosensors]]
+
==Online learning==
  
[[User:Jarle Pahr/BioBricks|BioBricks]]
+
https://www.coursera.org/course/usefulgenetics
  
[[User:Jarle Pahr/Bioconductor|BioConductor]]
+
http://www.skillshare.com/
  
[[User:Jarle Pahr/Biofilms|Biofilms]]
+
'''Portals:'''
  
[[User:Jarle Pahr/Biofuel|Biofuel]]
+
Saylor: http://www.saylor.org/majors/biology/
  
[[User:Jarle Pahr/Biopython|BioPython]]
+
http://www.class-central.com/
  
[[User:Jarle Pahr/BioStars|BioStars]]
+
http://www.core.org.cn
  
[[User:Jarle Pahr/Biocurious|Biocurious]]
+
https://www.coursera.org/
  
[[User:Jarle Pahr/Broad_Institute|Broad Institute]]
+
MIT Open Courseware: http://ocw.mit.edu/index.htm
  
[[User:Jarle Pahr/Big_data|Big data]]
+
Udacity:https://www.udacity.com/
  
[[User:Jarle Pahr/BWA|Burrows-Wheeler Aligner]]
+
EdX: https://www.edx.org/courses
  
[[User:Jarle Pahr/BWT|Burrows-Wheeler Transform]]
+
Khan academy: https://www.khanacademy.org
  
[[User:Jarle Pahr/Biological_computation|Biological computation]]
+
http://www.bioinformatics.org/edu/course/
  
[[User:Jarle Pahr/Bioprospecting|Bioprospecting]]
+
'''Specific courses:'''
  
[[User:Jarle Pahr/Bioinformatics|Bioinformatics]]
+
Computational investing course: https://www.coursera.org/course/compinvesting1
  
[[User:Jarle Pahr/BOW|Bioinformatics on Windows]]
+
Linear and discrete optimization course: https://www.coursera.org/course/linearopt
  
[[User:Jarle Pahr/Bowtie|Bowtie]]
+
https://www.coursera.org/course/macroeconomics
  
[[User:Jarle Pahr/Bitesize|Bitesize Biology]]
+
Bioinformatics algorithms: https://www.coursera.org/course/bioinformatics
  
[[User:Jarpe Pahr/BAMBI|BAMBI]]
+
Financial Engineering: https://www.coursera.org/course/fe
  
[[User:Jarpe Pahr/BAMBI#BAMBI-LAST|BAMBI-LAST]]
+
A beginner's guide to irrational behavior: https://www.coursera.org/course/behavioralecon
  
[[User:Jarpe Pahr/BAMBI#BAMBI-FAST|BAMBI-FAST]]
+
Computational molecular evolution: https://www.coursera.org/course/molevol
  
[[User:Jarle Pahr/BAMTools|BAMTools]]
+
https://www.coursera.org/course/netsysbio
  
[[User:Jarle Pahr/BLASR|BLASR]]
+
Introduction to Systems Biology: https://www.coursera.org/course/sysbio
  
[[User:Jarle Pahr/BLAST|BLAST]]
+
Biostatistics bootcamp: https://www.coursera.org/course/biostats
  
[[User:Jarle Pahr/BLAT|BLAT]]
+
High performance scientific computing: https://www.coursera.org/course/scicomp
  
[[User:Jarle Pahr/Blogs|Blogs]]
+
==Language==
  
[[User:Jarle Pahr/Books|Books]]
 
  
[[User:Jarle Pahr/BPDR|BPDR]]
+
===Chinese===
  
[[User:Jarle Pahr/Bistability|Bistability]]
+
http://english.cntv.cn/learnchinese/
  
[[User:Jarle Pahr/Buffers|Buffers]]
+
http://popupchinese.com/
  
[[User:Jarle Pahr/Business|Business]]
+
http://www.sinosplice.com/
  
 +
http://www.clearchinese.com/learn-chinese
  
[[User:Jarle Pahr/Curation|Biocuration]]
+
http://www.instantspeakchinese.com/
  
===C===
+
"The 5 stages of learning chinese:" http://www.sinosplice.com/learn-chinese/stages-to-learning-chinese
  
 +
Courses:
  
[[User:Jarle Pahr/CAD|Computer Aided Design]]
+
http://www.languageinfusion.no/kinesiskonline.php?gclid=CNfCsP_N3LYCFc5a3godPh0ATQ
  
[[User:Jarle Pahr/CAM|Computer Aided Manufacturing]]
+
http://www.learn-mandarin-help.com/software-to-learn-chinese.html
  
[[User:Jarle Pahr/COBRA|COBRA]]
+
http://www.rocketlanguages.com/chinese/premium/index.php?hop=jon1573
  
[[User:Jarle Pahr/Copasi|COPASI]]
+
http://chinesepod.com/
  
[[User:Jarle Pahr/Cancer|Cancer]]
+
http://www.sinosplice.com/learn-chinese/an-insiders-look-at-chinesepod
  
[[User:Jarle Pahr/Cell_Designer|Cell Designer]]
+
http://store.instantimmersion.com/chinese.html
  
[[User:Jarle Pahr/Chemistry|Chemistry]]
+
http://www.fluenz.com/languages/mandarin/learn-mandarin/
  
[[User:Jarle Pahr/Chromosomal_integration|Chromosomal integration]]
+
http://www.pimsleur.com/learn-mandarin-chinese
  
[[User:Jarle Pahr/Calculations|Calculations]]
+
http://www.learn-mandarin-help.com/rosetta-stone-mandarin.html
  
[[User:Jarle Pahr/Centrifugation|Centrifugation]]
+
http://www.amazon.com/Rosetta-Stone-Chinese-Mandarin-Level/dp/1608299643
  
[[User:Jarle Pahr/Characterising|Characterising]]
+
http://www.rosettastone.eu/lp/brand/?cid=se-ggeu1b13&rd=0
  
[[User:Jarle Pahr/Chassis|Chassis]]
+
http://www.learn-mandarin-help.com/
  
[[User:Jarle Pahr/Checklists|Checklists]]
+
http://www.fsi-language-courses.org/Content.php
  
[[User:Jarle Pahr/Chemicals|Chemicals]]
+
Foreign Service Institute language courses - Standard Chinese, a modular approach: http://www.fsi-language-courses.org/Content.php?page=Chinese
  
[[User:Jarle Pahr/CitedNotRead|CitedNotRead]]
+
http://ocw.mit.edu/courses/foreign-languages-and-literatures/21f-101-chinese-i-regular-spring-2006/
  
[[User:Jarle Pahr/CNC|CNC]]
 
  
[[User:Jarle Pahr/CNS|Cell Nature Science]]
 
  
[[User:Jarle Pahr/Companies|Companies]]
+
Books:
  
[[User:Jarle Pahr/Competent_cells|Competent cells]]
 
  
[[User:Jarle Pahr/Competitions|Competitions]]
+
http://www.amazon.com/gp/product/7800521346/ref=cm_cr_asin_lnk
  
[[User:Jarle Pahr/Conferences|Conferences]]
+
New Practical Chinese Reader Textbook 1: http://www.amazon.com/New-Practical-Chinese-Reader-Textbook/dp/7561910401
  
[[User:Jarle Pahr/Contamination|Contamination]]
+
New Practical Chinese Reader series: http://www.sinoliterature.co.uk/english/index.aspx?category=68&gclid=CO2pyuLB3LYCFcNQ3god_CgAHg
  
[[User:Jarle Pahr/Costs|Costs]]
+
Reading/Writing:  
  
[[User:Jarle Pahr/Cloning|Cloning]]
+
http://www.amazon.com/Reading-Writing-Chinese-Simplified-Character/dp/0804835098/ref=cm_cr-mr-title
  
[[User:Jarle Pahr/Cloud_computing|Cloud computing]]
+
http://www.quickmandarin.com/chinesepinyintable/
  
[[User:Jarle Pahr/Computation|Computation]]
+
Dictionaries:
  
[[User:Jarle Pahr/Colicins|Colicins]]
+
http://www.nciku.com/
  
[[User:Jarle Pahr/Commerce|Commerce]]
+
http://www.zhongwen.com/
  
[[User:Jarle Pahr/Courses|Courses]]
 
  
[[User:Jarle Pahr/Control_theory|Control theory]]
+
Speaking:
  
[[User:Jarle Pahr/Cufflinks|Cufflinks]]
+
SpeakGoodChinese: http://www.speakgoodchinese.org/
  
[[User:Jarle Pahr/Cytoscape|Cytoscape]]
+
==Synthetic Biology==
  
===D===
+
See [[User:Jarle Pahr/Synthetic_biology|Synthetic Biology]]
  
[[User:Jarle Pahr/Data|Data]]
+
==Biological part collections==
  
[[User:Jarle Pahr/Data_analysis|Data analysis]]
+
http://partsregistry.org
  
[[User:Jarle Pahr/Data_mining|Data mining]]
+
https://biobricks.org/bpa/find-a-part/
  
[[User:Jarle Pahr/Databases|Databases]]
+
https://registry.synberc.org/
  
[[User:Jarle Pahr/dbSNP|dbSNP]]
+
https://public-registry.jbei.org/ (http://www.ncbi.nlm.nih.gov/pubmed/22718978)
  
[[User:Jarle Pahr/de_Bruijn_graphs|de Bruijn graphs]]
+
==DIY Bio/Citizen science==
  
[[User:Jarle Pahr/Degradation_tags|Degradation tags]]
 
  
[[User:Jarle Pahr/DNA|DNA]]
+
See [[User:Jarle Pahr/DIYBio|DIY Bio]]
  
[[User:Jarle Pahr/DNA_analysis|DNA analysis]]
+
http://citizensciencequarterly.com/
  
[[User:Jarle Pahr/DNA_assembly|DNA assembly]]
+
==Art and Strategy==
  
[[User:Jarle Pahr/DNA_polymerase|DNA polymerase]]
+
http://biocouture.co.uk/about/
  
[[User:Jarle Pahr/Discovar|Discovar]]
+
Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp
  
[[User:Jarle Pahr/DIYBio|DIY Bio]]
+
http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment
  
===E===
+
http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/
  
[[User:Jarle Pahr/Education|Education]]
+
http://blog.arduino.cc/2013/05/19/the-mood-lamp-recognizes-your-facial-expressions-and-turns-them-into-light/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer7d04e
  
[[User:Jarle Pahr/Electrophoresis|Electrophoresis]]
+
http://thefinchandpea.com/2010/06/20/what-the-end-of-the-world-says-about-science/
  
[[User:Jarle Pahr/Electronics|Electronics]]
+
http://thefinchandpea.com/2013/08/04/sunday-poem-lord-byrons-post-apocalyptic-vision/
  
[[User:Jarle Pahr/ELN|ELN]]
+
==Personal genomics==
  
[[User:Jarle Pahr/Emboss|EMBOSS]]
+
https://www.23andme.com/
  
[[User:Jarle Pahr/Epigenetics|Epigenetics]]
+
http://www.23andyou.com
  
[[User:Jarle Pahr/Errors|Errors]]
+
http://www.genomesunzipped.org/
  
[[User:Jarle Pahr/eQTL|expression Quantiative Trait Loci]]
+
uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
  
[[User:Jarle Pahr/ERP|Enterprise Resource Planning]]
+
http://www.personalgenomes.org/
  
[[User:Jarle Pahr/Euler|EULER]]
+
==Companies==
  
[[User:Jarle Pahr/Ethics|Ethics]]
+
Evolutionary Solutions: http://www.evosol.co/
  
[[User:Jarle Pahr/Experiments|Experiments]]
+
http://www.allelebiotech.com/allele3/index.php
  
[[User:Jarle Pahr/Experimental_design|Experimental design]]
+
Era7: http://era7bioinformatics.com/en/index.cfm
  
[[User:Jarle Pahr/Expression|Expression]]
+
DNA electronics: http://dnae.co.uk/
  
[[User:Jarle Pahr/Exome_sequencing|Exome_sequening]]
+
Genome Compiler: http://www.genomecompiler.com/
  
[[User:Jarle Pahr/Equipment|Equipment]]
+
http://www.strandls.com
  
[[User:Jarle Pahr/Evolution|Evolution]]
+
http://www.novozymes.com/en/Pages/default.aspx
  
[[User:Jarle Pahr/E_coli|E. coli]]
+
http://www.genabler.com
  
===F===
+
http://www.syntheticgenomics.com/
  
[[User:Jarle Pahr/Fame|FAME]]
+
BGI: http://www.genomics.cn/en/index
  
[[User:Jarle Pahr/FastPCR|FastPCR]]
+
Gen9: http://gen9bio.com/
  
[[User:Jarle Pahr/Favorites|Favorites]]
+
DNA 2.0: https://www.dna20.com
  
[[User:Jarle Pahr/FFL|Feed-Forward Loops]]
+
Integrated DNA Technologies (IDT): http://eu.idtdna.com/site
  
[[User:Jarle Pahr/Food|Food]]
+
GenScript: http://www.genscript.com/
  
[[User:Jarle Pahr/Forums|Forums]]
+
Desktop Genetics: http://www.deskgen.com
  
[[User:Jarle Pahr/FRET|FRET]]
+
Ginkgo Bioworks: http://ginkgobioworks.com/
  
[[User:Jarle Pahr/Forensics|Forensics]]
+
Biofab: http://www.biofab.org/
  
[[User:Jarle Pahr/Future_products|Future products]]
+
http://www.knome.com/
  
[[User:Jarle Pahr/Flow_cytometry|Flow cytometry]]
+
http://www.nucleics.com/
  
[[User:Jarle Pahr/Fluxomics|Fluxomics]]
+
https://www.transcriptic.com/
  
[[User:Jarle Pahr/FBA|Flux Balance Analysis]]
+
Cambrian Genomics:  
 +
https://angel.co/cambrian-genomics
 +
http://cambriangenomics.com/
  
===G===
+
http://www.genologics.com
  
[[User:Jarle Pahr/Galaxy|Galaxy]]
+
==Suppliers==
  
[[User:Jarle Pahr/GATK|GATK]]
+
http://store.p212121.com/
  
[[User:Jarle Pahr/Games|Games]]
+
http://www.biosciencetools.com/
  
[[User:Jarle Pahr/GenBank|GenBank]]
+
http://www.laboratory-journal.com/
  
[[User:Jarle Pahr/Genes|Genes]]
+
www.labx.com
  
[[User:Jarle Pahr/Gene_deletion|Gene deletion]]
+
http://www.oxfordgenetics.co.uk/
  
[[User:Jarle Pahr/GeneDesigner|GeneDesigner]]
+
BioBasic: http://store.biobasic.com/
  
[[User:Jarle Pahr/Gene_prediction|Gene prediction]]
+
Promega: http://no.promega.com/
  
[[User:Jarle Pahr/Genetic_circuits|Genetic circuits]]
+
Qiagen: http://www.qiagen.com/
  
[[User:Jarle Pahr/GRN|Gene regulatory networks]]
+
DongSheng Biotech: http://dongshengbio.com/en/index.asp
  
[[User:Jarle Pahr/Gene_therapy|Gene therapy]]
+
Macrogen Inc.: http://www.macrogen.com/eng/index/
  
[[User:Jarle Pahr/Genetic_engineering|Genetic engineering]]
+
Carolina Biological: http://www.carolina.com/
  
[[User:Jarle Pahr/Genomes|Genomes]]
+
Epoch Life Sciences: http://www.epochlifescience.com/Default.aspx
  
[[User:Jarle Pahr/Genome_compiler|Genome compiler]]
+
http://www.hometrainingtools.com/
  
[[User:Jarle Pahr/Genome_browsers|Genom browsers]]
+
http://www.labsupplymall.com/
  
[[User:Jarle Pahr/Genomics|Genomics]]
+
United Nuclear: http://www.unitednuclear.com/
  
[[User:Jarle Pahr/GLF|Genotype Likelihood Format]]
+
New England Biolabs: www.neb.com
  
[[User:Jarle Pahr/Graphics|Graphics]]
+
Elemental Scientific: http://www.elementalscientific.net/store/Scripts/default.asp
  
[[User:Jarle Pahr/Gurobi|Gurobi]]
+
Jena BioScience: http://www.jenabioscience.com/
  
[[User:Jarle Pahr/GWAS|Genome Wide Association Studies]]
+
http://www.synthesisgene.com/
  
[[User:Jarle Pahr/GMO|GMO]]
+
Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152
  
[[User:Jarle Pahr/GFP|GFP]]
+
http://www.millipore.com/index.do
  
[[User:Jarle Pahr/Git|Git]]
+
See also http://www.made-in-china.com/
  
[[User:Jarle Pahr/Genetics|Genetics]]
+
Open Biotechnology: http://www.openbiotech.com/
  
[[User:Jarle Pahr/GATK|GATK]]
+
http://www.metabion.com/home/index.php
  
[[User:Jarle Pahr/Genealogy|Genealogy]]
+
http://bostonbioproducts.com/
  
[[User:Jarle Pahr/Graph_theory|Graph theory]]
+
http://www.sbsbio.com/english/dnahc.html
  
[[User:Jarle Pahr/Growth_media|Growth media]]
+
http://www.interfarm.no/produkter/
  
[[User:Jarle Pahr/GWAS|GWAS]]
+
http://www.iorodeo.com/
  
===H===
+
'''Used equipment vendors:'''
  
[[User:Jarle Pahr/Hadoop|Hadoop]]
+
http://www.labrecyclers.com/index.html
  
[[User:Jarle Pahr/HaveRead|Have Read]]
+
==Useful links==
 +
*[[OpenWetWare:Welcome|Introductory tutorial]]
 +
*[[Help|OpenWetWare help pages]]
  
[[User:Jarle Pahr/Hackerspaces|Hackerspaces]]
 
  
[[User:Jarle Pahr/Hardware|Hardware]]
+
===Conferences and meetings===
  
[[User:Jarle Pahr/Hardware|Health]]
 
  
[[User:Jarle Pahr/HTS|High Throughput Sequencing]]
 
  
[[User:Jarle Pahr/HSL|Homoserine lactones]]
+
See [[User:Jarle Pahr/Conferences|Conferences]]
  
[[User:Jarle Pahr/History_of_science|History of science]]
+
===Scientific challenges and competitions===
  
===I===
+
CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/
  
[[User:Jarle Pahr/Ideas|Ideas]]
+
Assemblathon
  
[[User:Jarle Pahr/IRC|IRC]]
+
Variathon: http://bioinf.dimi.uniud.it/variathon
  
[[User:Jarle Pahr/IGV|IGV]]
+
Alignathon
  
[[User:Jarle Pahr/Illumina|Illumina]]
+
Sequence squeeze: http://www.sequencesqueeze.org/
  
[[User:Jarle Pahr/Isaac|Isaac]]
+
===Resources for researchers===
  
[[User:Jarle Pahr/iGEM|iGEM]]
+
http://www.protocol-online.org/science-forums-2/Dissertation-and-Paper-Writing/
  
[[User:Jarle Pahr/in vitro|in vitro]]
+
http://www.protocol-online.org/science-forums-2/Career-Advice/
  
[[User:Jarle Pahr/Industrial_ecology|Industrial ecology]]
+
https://www.researchgate.net
  
[[User:Jarle Pahr/Isolation|Isolation]]
+
http://friendfeed.com/the-life-scientists
  
[[User:Jarle Pahr/Invisibility|Invisibility]]
+
http://nigerianbioscientist.com/
  
[[User:Jarle Pahr/Instructables|Instructables]]
+
===Educational resources===
 +
http://www.bioinformatics.nl/molbi/SimpleCloningLab/index.htm
  
[[User:Jarle Pahr/Image_analysis|Image analysis]]
+
ROSALIND Bioinformatics challenges: http://rosalind.info/problems/locations/
  
===K===
+
Project Euler: http://projecteuler.net/
  
[[User:Jarle Pahr/Kits|Kits]]
+
AddGene molecular biology reference: http://www.addgene.org/mol_bio_reference/
  
 +
https://www.manylabs.org/
  
[[User:Jarle Pahr/Khmer|Khmer]]
+
http://www.dnalabbook.co.uk/
  
===L===
+
=Wiki sites=
  
[[User:Jarle Pahr/Law|Law]]
+
http://www.scholarpedia.org
  
[[User:Jarle Pahr/LIMS|LIMS]]
+
SNPedia.com
  
[[User:Jarle Pahr/Linux|Linux]]
+
http://www.wikigenes.org
  
[[User:Jarle Pahr/LAST|LAST]]
+
http://ecoliwiki.net
  
[[User:Jarle Pahr/Lean|Lean]]
+
http://www.phylocommons.org/
  
[[User:Jarle Pahr/Laboratory_software|Laboratory software]]
+
===Discussion and communities===
  
[[User:Jarle Pahr/LIC|LIC]]
+
===Apps===
  
[[User:Jarle Pahr/Language|Language]]
+
mPartsregistry: http://mpartsregistry.appspot.com
  
[[User:Jarle Pahr/LaTeX|LaTeX]]
+
===Persons/Research groups===
  
[[User:Jarle Pahr/lablessons|Lab lessons]]
+
http://genefish.wikispaces.com/
  
[[User:Jarle Pahr/Lac_operon|Lac operon]]
+
Mark Pallen: http://www2.warwick.ac.uk/fac/med/research/microinfect/staff/pallengroup/
  
[[User:Jarle Pahr/Lean|Lean]]
+
Chris Anderson lab: https://andersonlab.qb3.berkeley.edu/
  
[[User:Jarle Pahr/Lux|Lux operon]]
+
Magni Paolo: http://www.labmedinfo.org/people/magni
  
[[User:Jarle Pahr/Ligation|Ligation]]
+
http://www.rpgroup.caltech.edu/publications/
  
[[User:Jarle Pahr/Liquid_handling|Liquid handling]]
+
Heng Li. "Alignment God".
  
===M===
+
Dworkin lab: https://www.msu.edu/~idworkin/publications.html
  
[[User:Jarle Pahr/Mapreduce|MapReduce]]
+
Titus Brown:  
  
[[User:Jarle Pahr/Metabolic_engineering|Metabolic engineering]]
+
Erlich lab: http://erlichlab.wi.mit.edu/index.html
  
[[User:Jarle Pahr/Metabolic_modelling|Metabolic modelling]]
+
Cristopher mason: http://www.masonlab.net/
  
[[User:Jarle Pahr/Mobile_tools|Mobile tools]]
+
http://openwetware.org/wiki/User:Vincent
  
[[User:Jarle Pahr/Microfluidics|Microfluidics]]
+
Markus Gershater
  
[[User:Jarle Pahr/MAQ|MAQ]]
+
http://www.princeton.edu/~ajlgroup/
  
[[User:Jarle Pahr/Microplates|Microplates]]
+
Heng Li
  
[[User:Jarle Pahr/Medicine|Medicine]]
+
Michael Cashel: https://science.nichd.nih.gov/confluence/display/pgd/Michael+Cashel+Lab
  
[[User:Jarle Pahr/Metabolic_burden|Metabolic burden]]
+
Jim Collins: http://www.bu.edu/abl/
  
[[User:Jarle Pahr/MOOC|Massive Open Online Courses]]
+
Jason Kelly: http://openwetware.org/wiki/Jason_Kelly
  
[[User:Jarle Pahr/MFA|Metabolic flux analysis]]
+
Tom Ellis: http://openwetware.org/wiki/User:Ellis
  
[[User:Jarle Pahr/Mutations|Mutations]]
+
George Church: http://arep.med.harvard.edu/gmc/
  
[[User:Jarle Pahr/Microscopy|Microscopy]]
+
Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html
  
[[User:Jarle Pahr/Models|Models]]
+
Chris Voigt
  
[[User:Jarle Pahr/Miniexperiments|Miniexperiments]]
+
Bernahrd Ø Pallsson: http://gcrg.ucsd.edu/Researchers/Palsson
  
[[User:Jarle Pahr/Modelling|Modelling]]
+
Tom Knight
  
[[User:Jarle Pahr/Motifs|Network motifs]]
+
Joe Felsenstein: http://www.gs.washington.edu/faculty/felsenstein.htm
 +
*Professor of Genome Sciences and Biology, University of Washington.
  
[[User:Jarle Pahr/Microbiology|Microbiology]]
+
Drew Endy: http://openwetware.org/wiki/User:Endy
  
===N===
+
Densmore lab: http://people.bu.edu/dougd/research.html
  
[[User:Jarle Pahr/Nested_feedback_loops|Nested feedback loops]]
+
Ron Weiss: http://groups.csail.mit.edu/synbio/people/professor-ron-weiss/
  
[[User:Jarle Pahr/Nanopore|Nanopore]]
+
Jean Peccoud
  
[[User:Jarle Pahr/Networks|Networks]]
+
Jonathan Eisen
  
[[User:Jarle Pahr/Norway|Norway]]
+
Martin Fusenegger
  
[[User:Jarle Pahr/Nutrition|Nutrition]]
+
Pamela Silver
  
[[User:Jarle Pahr/Negative_results|Negative results]]
+
Rob Carlson
  
[[User:Jarle Pahr/Neuroscience|Neuroscience]]
+
Ethan Perlstein: http://www.perlsteinlab.com/
  
[[User:Jarle Pahr/NMR|NMR]]
+
Anthony Evans
  
[[User:Jarle Pahr/Noise|Noise]]
+
Nick Loman:  
  
===O===
+
http://pathogenomics.bham.ac.uk/clinicogenomics/
  
[[User:Jarle Pahr/Organisms|Organisms]]
+
http://pathogenomics.bham.ac.uk/blog/author/nick/
  
[[User:Jarle Pahr/OMIM|OMIM]]
+
Titus Brown: http://ivory.idyll.org/blog/category/science.html
  
[[User:Jarle Pahr/Oscillation|Oscillation]]
+
Lex Nedebragt:
  
[[User:Jarle Pahr/Ontologies|Ontologies]]
+
http://contig.wordpress.com/
  
[[User:Jarle Pahr/OGE|Open Genomics Engine]]
+
https://twitter.com/lexnederbragt
  
[[User:Jarle Pahr/Openwetware|OpenWetWare]]
+
Manual Corpas:
  
[[User:Jarle Pahr/OpenWorm|OpenWorm]]
+
Barry L Wanner: https://www.bio.purdue.edu/molecular_biosciences/directory.php?refID=30
 +
*Made many E. coli strains.
  
[[User:Jarle Pahr/Optimization|Optimization]]
+
Andrew Hessel: http://andrewhessel.com/
  
[[User:Jarle Pahr/Optogenetics|Optogenetics]]
+
===Societies and associations===
  
[[User:Jarle Pahr/Oligonucleotides|Oligonucleotides]]
+
Society for applied microbiology: http://www.sfam.org.uk/
  
[[User:Jarle Pahr/Open_science|Open science]]
+
American Association for Clinical Chemistry : http://www.aacc.org/Pages/default.aspx
  
[[User:Jarle Pahr/Online_services|Online services]]
+
Royal Society of Chemistry: http://www.rsc.org/
  
[[User:Jarle Pahr/Open_source|Open source]]
+
Society for general microbiology: http://www.sgm.ac.uk/
  
===P===
+
American society for microbiology: http://www.asm.org/
  
[[User:Jarle Pahr/Pathogens|Pathogens]]
+
Norsk Kjemisk selskap: http://www.kjemi.no/
  
[[User:Jarle Pahr/Pathways|Pathways]]
+
International Society for Systems Biology: http://www.issb.org/
  
[[User:Jarle Pahr/People|People]]
+
Genetics Society of America: http://www.genetics-gsa.org/
  
[[User:Jarle Pahr/Performance|Performance]]
+
British Society for Gene and Cell Therapy: https://www.facebook.com/BSGCT
  
[[User:Jarle Pahr/Peccoud|Peccoud]]
+
American Society of Human Genetics (ASHG):
  
[[User:Jarle Pahr/Phyre|Phyre]]
+
Society for Molecular Biology and Evolution (SMBE): http://www.smbe.org/
  
[[User:Jarle Pahr/Phred|Phred]]
+
===Publications===
  
[[User:Jarle Pahr/Photosynthesis|Photosynthesis]]
 
  
[[User:Jarle Pahr/Phenotype_switching|Phenotype switching]]
+
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
+
|-
[[User:Jarle Pahr/Philosophy|Philosophy]]
+
! Journal name!! Publisher !! Open access status !! Link
 
+
|-
[[User:Jarle Pahr/PID|PID]]
+
| ACS Synthetic Biology || American Chemical Society ||No ||  http://pubs.acs.org/journal/asbcd6
 
+
|-
[[User:Jarle Pahr/Plink|Plink]]
+
| Bioengineered (Previously: Bioengineered bugs) || Landes Bioscience ||Partial ||http://dev.landesbioscience.com/journals/bioe/
 
+
|-
[[User:Jarle Pahr/Pipetting|Pipetting]]
+
|Bioinformatics||Oxford Journals|| ||http://bioinformatics.oxfordjournals.org/
 
+
|-
[[User:Jarle Pahr/Projects|Projects]]
+
|Biology Open||Company of Biologists||Yes||http://bio.biologists.org/
 
+
|-
[[User:Jarle Pahr/pH|pH]]
+
|BMC Medical Genomics||BMC||Yes||http://www.biomedcentral.com/bmcmedgenomics/
 
+
|-
[[User:Jarle Pahr/Patents|Patents]]
+
|BMC Proceedings||BMC||Yes||http://www.biomedcentral.com/bmcproc
 
+
|-
[[User:Jarle Pahr/Persistence|Persistence]]
+
| PLOS One  ||Public Library of Science || Yes ||http://www.plosone.org/
 
+
|-
[[User:Jarle Pahr/Petri_nets|Petri nets]]
+
| Nucleic Acids Research|| Oxford Journals || Yes || http://nar.oxfordjournals.org/
 
+
|-
[[User:Jarle Pahr/Plasmids|Plasmids]]
+
|BMC Systems Biology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcsystbiol/
 
+
|-
[[User:Jarle Pahr/Phylogenetics|Phylogenetics]]
+
|BMC Microbiology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcmicrobiol
 
+
|-
[[User:Jarle Pahr/Posters|Posters]]
+
|Cell||Cell Press|| ||http://www.cell.com/
 
+
|-
[[User:Jarle Pahr/Promoters|Promoters]]
+
|Cell Reports||Cell Press ||Yes||http://cellreports.cell.com/
 
+
|-
[[User:Jarle Pahr/Protocols|Protocols]]
+
|The EMBO Journal||Nature Publishing Group ||No||http://www.nature.com/emboj/index.html
 
+
|-
[[User:Jarle Pahr/PCR|PCR]]
+
|Frontiers in Synthetic Biology||Nature Publishing Group|| ||http://www.frontiersin.org/Synthetic_Biology/about
 
+
|-
[[User:Jarle Pahr/Programming|Programming]]
+
|Genetics||Genetics Society of America|| ||http://www.genetics.org/
 
+
|-
[[User:Jarle Pahr/Python|Python]]
+
|G3: Genes, Genomes, Genetics Mission ||Genetics Society of America|| ||http://www.g3journal.org/
 
+
|-
===R===
+
|Genome Research||Cold Spring Harbor Press||Partial (6 month embargo)|| http://genome.cshlp.org/
 
+
|-
[[User:Jarle Pahr/R|R]]
+
|Genome Biology||BMC||Yes||http://genomebiology.com/
 
+
|-
[[User:Jarle Pahr/Raspberry_pi|Raspberry pi]]
+
|Genome Medicine||BioMedCentral||Yes||http://genomemedicine.com/
 
+
|-
[[User:Jarle Pahr/Ray|Ray assembler]]
+
|Journal of Experimental Biology||Company of Biologists||http://jeb.biologists.org/
 
+
|-
[[User:Jarle Pahr/RNA|RNA]]
+
|Journal of molecular biology||Elsevier ||Partial||http://www.journals.elsevier.com/journal-of-molecular-biology/
 
+
|-
[[User:Jarle Pahr/RNAseq|RNAseq]]
+
|Journal of biological chemistry||American Society for Biochemistry and Molecular Biology.  ||No||http://www.jbc.org/
 
+
|-
[[User:Jarle Pahr/Refuted|Refuted]]
+
|Journal of bacteriology||American Society for Microbiology ||No||http://jb.asm.org/
 
+
|-
[[User:Jarle Pahr/Regulatos|Regulators]]
+
|Journal of Bioscience and Engineering||  || ||http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
 
+
|-
[[User:Jarle Pahr/Resources|Resources]]
+
|Journal of clinical microbiology||American Society for Microbiology||No||http://jcm.asm.org/
 
+
|-
[[User:Jarle Pahr/Ribosome|Ribosome]]
+
|mBio||ASM||Yes||http://mbio.asm.org/
 
+
|-
[[User:Jarle Pahr/Riboswitches|Riboswitches]]
+
|Methods||Elsevier||No||http://www.journals.elsevier.com/methods
 
+
|-
[[User:Jarle Pahr/Robotics|Robotics]]
+
|Microbiology||SGM/HighWire Press||No||http://mic.sgmjournals.org/
 
+
|-
[[User:Jarle Pahr/Robustness|Robustness]]
+
|Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology Reviews||ASM|| ||mmbr.asm.org
 
+
|-
[[User:Jarle Pahr/Research_tools|Research tools]]
+
|Metabolic Engineering||Elsevier||Partial||http://www.journals.elsevier.com/metabolic-engineering/
 
+
|-
[[User:Jarle Pahr/Questions|Research questions]]
+
|Molecular Systems Biology||EMBO/Nature Publishing Group||Yes||http://www.nature.com/msb/index.html||
 
+
|-
[[User:Jarle Pahr/Questionable|Questionable]]
+
|PLOS Computational Biology||Public Library of Science||Yes||http://www.ploscompbiol.org/
 
+
|-
[[User:Jarle Pahr/Recipes|Recipes]]
+
|PLOS Pathogens||PLOS||Yes||http://www.plospathogens.org/
 
+
|-
[[User:Jarle Pahr/Restriction|Restriction]]
+
|Proceedings of the National Academy of Sciences||National Academy of Sciences||No||http://www.pnas.org/
 
+
|-
[[User:Jarle Pahr/Retractions|Retractions]]
+
|Protein expression and purification||Elsevier||No||http://www.sciencedirect.com/science/journal/10465928
 
+
|-
[[User:Jarle Pahr/RNA|RNA]]
+
|Genome Announcements||ASM||Yes||http://genomea.asm.org/
 
+
|-
[[User:Jarle Pahr/RNA_polymerase|RNA polymerase]]
+
|Futures||Elsevier||?||http://www.sciencedirect.com/science/journal/00163287
 
+
|-
[[User:Jarle Pahr/RBS|RBS]]
+
|Microbial Cell Factories||BioMedCentral||Yes||http://www.microbialcellfactories.com/
 
+
|-
===S===
+
|Engineering Studies||Taylor & Francis|| ?||http://www.tandfonline.com/loi/test20
 
+
|-
[[User:Jarle Pahr/Sanger|Sanger sequencing]]
+
|FEMS Microbiology Reviews|| || ||http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
 
+
|-
[[User:Jarle Pahr/Safety|Safety]]
+
|Nature Biotechnology||Nature Publishing Group||No||http://www.nature.com/nbt/index.html
 
+
|-
[[User:Jarle Pahr/Search|Search]]
+
|Nature Genetics||Nature Publishing group||No||http://www.nature.com/ng/index.html
 
+
|-
[[User:Jarle Pahr/Skills|Skills]]
+
|Plasmid||Elsevier||No||http://www.journals.elsevier.com/plasmid/
 
+
|-
[[User:Jarle Pahr/Sequencing|Sequencing]]
+
|Journal of Computational Biology||Liebert Publishing||No||http://www.liebertpub.com/CMB
 
+
|-
[[User:Jarle Pahr/Scientific_computing|Scientific computing]]
+
|Trends in Biochemical Sciences||Elsevier|| ||http://www.sciencedirect.com/science/journal/09680004
 
+
|-
[[User:Jarle Pahr/SLIC|SLIC]]
+
|Trends in Microbiology||Elsevier/Cell Press|| ||http://www.sciencedirect.com/science/journal/0966842X
 
+
|-
[[User:Jarle Pahr/Slides|Slides]]
+
|Molecular Genetics & Genomic Medicine||Wiley||Yes||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
 
+
|-
[[User:Jarle Pahr/Stampy|Stampy]]
+
|Molecular genetics and genomics||Springer Verlag|| ||http://link.springer.com/journal/438
 
+
|-
[[User:Jarle Pahr/SMRT|SMRT]]
+
|Biochemistry and Molecular Biology Education||Wiley||No||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
 
+
|-
[[User:Jarle Pahr/SNP|SNP]]
+
|Current opinion in chemical biology||Elsevier|| ||http://www.sciencedirect.com/science/journal/13675931
 
+
|-
[[User:Jarle Pahr/SOAP|SOAP]]
+
|New England Journal of Medicine||NEJM Group|| ||http://www.nejm.org/
 
+
|-
[[User:Jarle Pahr/Spades|Spades]]
+
|Systems and Synthetic Biology||Springer|| ||http://link.springer.com/journal/11693
 
+
|-
[[User:Jarle Pahr/Storage|Storage]]
+
|Scientific Reports||Nature Publishing Group||Yes||http://www.nature.com/srep/index.html
 
+
|}
[[User:Jarle Pahr/Single_cell|Single cell technologies]]
 
 
 
[[User:Jarle Pahr/Social_web|Social web]]
 
 
 
[[User:Jarle Pahr/Scientific_computing|Scientific computing]]
 
 
 
[[User:Jarle Pahr/Software|Software]]
 
 
 
[[User:Jarle Pahr/Stringent_response|Stringent response]]
 
 
 
[[User:Jarle Pahr/SAM|SAM]]
 
 
 
[[User:Jarle Pahr/SWA|SWA]]
 
 
 
[[User:Jarle Pahr/SGA|SGA]]
 
 
 
[[User:Jarle Pahr/SAMTools|SAMTools]]
 
 
 
[[User:Jarle Pahr/Statistics|Statistics]]
 
 
 
[[User:Jarle Pahr/Stocks|Stocks]]
 
 
 
[[User:Jarle Pahr/Strains|Strains]]
 
 
 
[[User:Jarle Pahr/Sterilization|Sterilization]]
 
 
 
[[User:Jarle Pahr/SVM|Support Vector Machines]]
 
 
 
[[User:Jarle Pahr/Synthetic_biology|Synthetic Biology]]
 
 
 
[[User:Jarle Pahr/Systems_biology|Systems Biology]]
 
 
 
[[User:Jarle Pahr/Simulations|Simulations]]
 
 
 
[[User:Jarle Pahr/Staden|Staden]]
 
 
 
===T===
 
 
 
[[User:Jarle Pahr/Tasks|Tasks]]
 
 
 
[[User:Jarle Pahr/Taxonomy|Taxonomy]]
 
 
 
[[User:Jarle Pahr/Technobabble|Technobabble]]
 
 
 
[[User:Jarle Pahr/Terminators|Terminators]]
 
 
 
[[User:Jarle Pahr/Transformation|Transformation]]
 
 
 
[[User:Jarle Pahr/Transcription|Transcription]]
 
 
 
[[User:Jarle Pahr/Translation|Translation]]
 
 
 
[[User:Jarle Pahr/Transposons|Transposons]]
 
 
 
[[User:Jarle Pahr/Theses|Theses]]
 
 
 
[[User:Jarle Pahr/ToRead|To Read]]
 
 
 
[[User:Jarle Pahr/Theses|Tutorials]]
 
 
 
[[User:Jarle Pahr/Turbidimetry|Turbidimetry]]
 
 
 
[[User:Jarle Pahr/Trinity|Trinity]]
 
 
 
 
 
===U===
 
 
 
[[User:Jarle Pahr/UGENE|UGENE]]
 
 
 
===V===
 
 
 
[[User:Jarle Pahr/Variant_calling|Variant calling]]
 
 
 
[[User:Jarle Pahr/Vectors|Vectors]]
 
 
 
[[User:Jarle Pahr/Velvet|Velvet]]
 
 
 
[[User:Jarle Pahr/Venter|Venter]]
 
 
 
[[User:Jarle Pahr/VCF|VCF]]
 
  
[[User:Jarle Pahr/Verification|Verification]]
 
  
[[User:Jarle Pahr/Version control|Version control]]
+
Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/
  
===W===
+
Computational and Structural Biotechnology Journal
  
[[User:Jarle Pahr/Weizman_Institute|Weizman Institute]]
 
  
[[User:Jarle Pahr/Writing|Writing]]
+
http://www.journalnetwork.org/journals/science-general/citizen-science/citizen-science-innovation.html
  
[[User:Jarle Pahr/Weighing|Weighing]]
+
Biotechniques: http://www.biotechniques.com/
  
[[User:Jarle Pahr/Wisdom|Wisdom]]
+
https://www.openlibhums.org/
  
[[User:Jarle Pahr/Wine|Wine]]
+
Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727
  
[[User:Jarle Pahr/Whateverhappenedto|Whateverhappenedto]]
+
http://www.g3journal.org/
  
[[User:Jarle Pahr/Work|Work]]
+
http://push.cwcon.org/
  
[[User:Jarle Pahr/Workflows|Workflows]]
+
eLife: http://elife.elifesciences.org/
  
===Y===
+
https://peerj.com/
  
[[User:Jarle Pahr/Yeast|Yeast]]
+
Faculty of 1000: http://f1000.com/
  
[[User:Jarle Pahr/Yoghurt|Yoghurt]]
 
  
 +
Social Science Research Network: http://www.ssrn.com/
  
'''Genes/molecules:'''
 
  
 +
Open access:
  
[[User:Jarle Pahr/GreA|GreA]]
+
http://en.wikipedia.org/wiki/List_of_open-access_journals
  
[[User:Jarle Pahr/IraP|IraP]]
+
http://scholarlyoa.com/
  
[[User:Jarle Pahr/DksA|DksA]]
+
http://www.doaj.org/
  
[[User:Jarle Pahr/RelA|RelA]]
+
http://www.opendoar.org/
  
[[User:Jarle Pahr/SpoT|SpoT]]
+
http://blogs.scientificamerican.com/guest-blog/2013/04/03/who-killed-the-preprint-and-could-it-make-a-return/
  
[[User:Jarle Pahr/Fis|Fis]]
+
Publication tools:
  
[[User:Jarle Pahr/RpoS|RpoS]]
+
https://collage.elsevier.com/
  
[[User:Jarle Pahr/LldR|LldR]]
+
Reference management / Social bookmarking:
  
==Projects==
+
http://www.mendeley.com/
  
[[User:Jarle Pahr/Notebook/ppGpp Msc|ppGpp MSc. project]]
+
http://www.citeulike.org/
  
==Organisms==
+
JabRef reference manager: http://jabref.sourceforge.net/
  
 +
===Publishers===
  
See [[User:Jarle Pahr/Organisms|Organisms]]
+
Springer
  
==Interesting articles==
+
Elsevier
[http://www.ncbi.nlm.nih.gov/pubmed/21847113 Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen]
 
  
[http://www.ncbi.nlm.nih.gov/pubmed/16330045 Environmentally controlled invasion of cancer cells by engineered bacteria]
+
CRC Press
  
[http://www.ncbi.nlm.nih.gov/pubmed/18263722 Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli]
+
Horizon Press
  
[http://www.cell.com/abstract/S0092-8674%2812%2900776-3 A Whole-Cell Computational Model Predicts Phenotype from Genotype]
+
===Databases/Repositories===
  
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11516.html Genetic programs constructed from layered logic gates in single cells]
+
PlasmID database: http://plasmid.med.harvard.edu/PLASMID/
  
==Research centres/labs==
+
Addgene plasmid repository: http://www.addgene.org/
  
Wyss institute: http://wyss.harvard.edu/
+
DNASU plasid repository: http://dnasu.asu.edu/DNASU/
  
Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/
+
The Open Construct Database: http://www.the-odin.com
  
Cold Spring Harbor Laboratory: http://www.cshl.edu/
+
Bionumbers - [http://bionumbers.hms.harvard.edu/default.aspx The database of useful biological numbers]
  
Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/
+
EcoCyc - E. coli K-12 MG1655 database: http://www.ecocyc.org/
  
Insititute for Systems Biology: https://www.systemsbiology.org
+
EcoGene: http://www.ecogene.org
  
Virginia Bioinformatics Institute: https://www.vbi.vt.edu/
+
JWS Online model database: http://jjj.biochem.sun.ac.za/database/
  
European Bioinformatics Institute: http://www.ebi.ac.uk/
+
http://systems-biology.org/resources/model-repositories/
  
ATCC: http://www.lgcstandards-atcc.org/
+
Genome-Scale metabolic network database: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm
  
European Molecular Biology Laboratory (EMBL): http://www.embl.de/
+
Array express: http://www.ebi.ac.uk/arrayexpress/
  
http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html
+
Rebase restriction enzyme database: http://rebase.neb.com/rebase/rebase.html
  
 +
1000 genomes project: http://browser.1000genomes.org/index.html
  
http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
+
BRENDA Enzymes: http://www.brenda-enzymes.info/
  
http://korflab.ucdavis.edu/
+
KEGG
  
==Research programs/projects==
+
GenBank
  
Statseq: http://www2.ab.wur.nl/statseq/
+
http://datadryad.org/
  
==Online learning==
+
http://www.cathdb.info/
  
https://www.coursera.org/course/usefulgenetics
+
===Codon usage===
  
http://www.skillshare.com/
+
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333
  
'''Portals:'''
+
Codon usage analyzer: http://www.bioinformatics.org/sms2/codon_usage.html
  
http://www.class-central.com/
+
===Other informational resources===
  
http://www.core.org.cn
+
National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html
  
https://www.coursera.org/
+
http://seqanswers.com
  
MIT Open Courseware: http://ocw.mit.edu/index.htm
+
NCBI vs EMBL vs DDBJ.: http://lib.bioinfo.pl/courses/view/151
  
Udacity:https://www.udacity.com/
+
The DDBJ/EMBL/GenBank Feature Table Definition: http://www.insdc.org/files/feature_table.html#1
  
EdX: https://www.edx.org/courses
+
http://openwetware.org/wiki/DNA - Contains many protocols
  
Khan academy: https://www.khanacademy.org
+
Bite Size Bio: http://bitesizebio.com/
  
http://www.bioinformatics.org/edu/course/
+
BenchFly: http://www.benchfly.com/
  
'''Specific courses:'''
+
http://biologicalworld.com/protocols.htm
  
Computational investing course: https://www.coursera.org/course/compinvesting1
+
http://www.methods.info/
  
Linear and discrete optimization course: https://www.coursera.org/course/linearopt
+
http://www.biotechdaily.com/
  
https://www.coursera.org/course/macroeconomics
+
http://www.zenbiology.com/
  
Bioinformatics algorithms: https://www.coursera.org/course/bioinformatics
+
http://www.my-whiteboard.com/
  
Financial Engineering: https://www.coursera.org/course/fe
+
http://lablife.org
  
A beginner's guide to irrational behavior: https://www.coursera.org/course/behavioralecon
+
http://www.molbiol-tools.ca/
  
Computational molecular evolution: https://www.coursera.org/course/molevol
+
http://www.molecularinfo.com/MTM/MTM.html
  
https://www.coursera.org/course/netsysbio
+
http://www.openhelix.com/ - Genomics and bioinformatics resources.
  
Introduction to Systems Biology: https://www.coursera.org/course/sysbio
+
===Programming===
  
Biostatistics bootcamp: https://www.coursera.org/course/biostats
+
BioPython: http://biopython.org/wiki/Main_Page
  
High performance scientific computing: https://www.coursera.org/course/scicomp
+
CodEval -  programming challenges: http://codeeval.com/
  
==Language==
+
===Law and ethics===
  
 +
http://www.genomicslawreport.com/
  
===Chinese===
+
American journal of Bioethics: http://www.tandfonline.com/toc/uajb20/current
  
http://english.cntv.cn/learnchinese/
+
IASB Code of Conduct for best practices in gene synthesis: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/code-of-conduct-for-best-practices-in-gene-synthesis/
  
http://popupchinese.com/
+
IASB - About Biosafety & Security: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/biosafety-biosecurity/
  
http://www.sinosplice.com/
+
Andrew W Torrance on DNA copyright: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2017670
  
http://www.clearchinese.com/learn-chinese
 
  
http://www.instantspeakchinese.com/
+
===Cloning===
  
"The 5 stages of learning chinese:" http://www.sinosplice.com/learn-chinese/stages-to-learning-chinese
+
SLIC, Gibson, CPEC and SLiCE assembly methods: http://j5.jbei.org/j5manual/pages/22.html
  
Courses:
+
RF cloning: http://www.rf-cloning.org/QandA.php
  
http://www.languageinfusion.no/kinesiskonline.php?gclid=CNfCsP_N3LYCFc5a3godPh0ATQ
+
PCR Primer design: http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm
  
http://www.learn-mandarin-help.com/software-to-learn-chinese.html
+
PCR: http://www.molbiol-tools.ca/PCR.htm
  
http://www.rocketlanguages.com/chinese/premium/index.php?hop=jon1573
+
OpenWetWare - designing primers: http://openwetware.org/wiki/Designing_primers
  
http://chinesepod.com/
+
PCR Guide: http://medicine.yale.edu/labs/henegariu/www/tavi/Guide.html
  
http://www.sinosplice.com/learn-chinese/an-insiders-look-at-chinesepod
+
PCR troubleshooting: http://medicine.yale.edu/labs/henegariu/www/tavi/Trblesht.html
  
http://store.instantimmersion.com/chinese.html
+
DNA Tm estimation methods: http://openwetware.org/wiki/Primer_Tm_estimation_methods
  
http://www.fluenz.com/languages/mandarin/learn-mandarin/
+
DNA stability: http://openwetware.org/wiki/DNA_stability
  
http://www.pimsleur.com/learn-mandarin-chinese
+
E. coli cloning checklist: http://openwetware.org/wiki/Cloning_Checklist
  
http://www.learn-mandarin-help.com/rosetta-stone-mandarin.html
+
Guide to Gibson assembly: http://www.synbio.org.uk/dna-assembly/guidetogibsonassembly.html
  
http://www.amazon.com/Rosetta-Stone-Chinese-Mandarin-Level/dp/1608299643
+
Primer design guidelines: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
  
http://www.rosettastone.eu/lp/brand/?cid=se-ggeu1b13&rd=0
+
===Sequencing===
  
http://www.learn-mandarin-help.com/
+
Design of sequencing primers: http://seqcore.brcf.med.umich.edu/doc/dnaseq/primers.html
  
http://www.fsi-language-courses.org/Content.php
+
Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi: http://biology.duke.edu/fungi/mycolab/primers.htm
  
Foreign Service Institute language courses - Standard Chinese, a modular approach: http://www.fsi-language-courses.org/Content.php?page=Chinese
+
GenScript DNA Sequencing Primers Design Tool: http://www.genscript.com/cgi-bin/tools/sequencing_primer_design
  
http://ocw.mit.edu/courses/foreign-languages-and-literatures/21f-101-chinese-i-regular-spring-2006/
+
===Software tools===
  
 +
Molecular Biology Freeware for Windows: http://molbiol-tools.ca/molecular_biology_freeware.htm#Graphic%20packages
  
 +
Molecular Biology & Bioinformatics Resources: http://library.weill.cornell.edu/eresources/molbio.html
  
Books:
+
Bioinformatics Tools and Resources for Biomedical Scientists and Students - http://www.changbioscience.com/virtualab.html
  
  
http://www.amazon.com/gp/product/7800521346/ref=cm_cr_asin_lnk
+
DNA copy number calculator: http://www.uri.edu/research/gsc/resources/cndna.html
  
New Practical Chinese Reader Textbook 1: http://www.amazon.com/New-Practical-Chinese-Reader-Textbook/dp/7561910401
+
Graphics software:
  
New Practical Chinese Reader series: http://www.sinoliterature.co.uk/english/index.aspx?category=68&gclid=CO2pyuLB3LYCFcNQ3god_CgAHg
+
===Systems Biology===
  
Reading/Writing:
+
http://systems-biology.org/
  
http://www.amazon.com/Reading-Writing-Chinese-Simplified-Character/dp/0804835098/ref=cm_cr-mr-title
+
Cytoscape: www.cytoscape.org
  
http://www.quickmandarin.com/chinesepinyintable/
+
CAIN stochastic simulations for chemical kinetics: http://cain.sourceforge.net/
  
Dictionaries:
+
COBRA Constraints-based modelling toolbox:  
  
http://www.nciku.com/
+
CellNetAnalyzer: http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html
  
http://www.zhongwen.com/
+
CellDesigner: http://celldesigner.org/
  
 +
OptFlux: http://www.optflux.org/
  
Speaking:
+
Systems Biology Markup Language: www.sbml.org
  
SpeakGoodChinese: http://www.speakgoodchinese.org/
+
SBML to LaTex report generator: http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/index.html
  
==Synthetic Biology==
+
Systems Biology Toolbox 2 for MATLAB: http://www.sbtoolbox2.org/main.php
  
www.synthetic-bestiary.com
+
http://www.sysbio.de/
  
http://www.synbioproject.org/
+
Handbook of Systems Biology: http://www.sciencedirect.com/science/book/9780123859440
  
http://www.synbiont.org/
+
Reflexive Systems Biology: http://portal.cbu.uib.no/rsb
  
Competitions and challenges:
+
===Bioinformatics & Annotation===
  
http://igem.org
+
Neural Network Promoter Prediction: http://www.fruitfly.org/seq_tools/promoter.html
  
http://genocon.org/
+
Artemis genome browser: http://www.sanger.ac.uk/resources/software/artemis/
  
http://www.ia-sb.eu/go/synthetic-biology/
+
BASYS Bacterial Annotation software: http://basys.ca/
  
LabGenius: www.labgeni.us
+
SoftBerry: http://linux1.softberry.com/berry.phtml
  
http://synbio.org.uk/
+
Promethease: http://snpedia.com/index.php/Promethease
  
Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/
+
GLIMMER microbial gene-finding system: http://www.cbcb.umd.edu/software/glimmer/
  
Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html
+
Promoter & termination site search tools: http://molbiol-tools.ca/Promoters.htm
  
TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering: http://synthetic-biology.bbn.com/tasbe.html
+
Phyre 2 - protein fold recognition: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
  
Raytheon BBN Synthetic biology publications: http://synthetic-biology.bbn.com/pubs.html'
+
FITBAR DNA binding protein binding site predictor: http://archaea.u-psud.fr/fitbar/
  
BBN Synthetic biology tools: https://synbiotools.bbn.com/
+
Simple Consensus Maker: http://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html
  
http://www.synberc.org/
+
Model SEED - blog: http://blog.theseed.org/model_seed/
  
http://www.teselagen.com/
+
Model SEED - Viewer: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView
  
==Biological part collections==
+
http://www.bioinformatics.org/
  
http://partsregistry.org
+
Plasmid map drawer: http://www.rf-cloning.org/savvy.php
  
https://biobricks.org/bpa/find-a-part/
+
EMBOSS ((European Molecular Biology Open Software Suite): http://bips.u-strasbg.fr/EMBOSS/
  
https://registry.synberc.org/
+
BioBrick -> GenBank converter: http://2010.igem.org/Team:Cambridge/Tools/GenBank
  
==DYI Bio/Citizen science==
 
  
http://blogs.plos.org/citizensci/2013/07/15/that-moment-when-you-realize-how-little-you-actually-know/
+
HMMER: http://hmmer.janelia.org/
  
http://www.cellslider.net/
+
Jcat Codon Adaption Tool: http://www.jcat.de/
  
http://madlab.org.uk/
+
===Cloning & Construction===
  
http://www.diygenomics.org/
+
The Constructor: http://2011.igem.org/Team:Wageningen_UR/Softwaretool/
  
http://hivebio.org/
+
NEBcutter: http://tools.neb.com/NEBcutter2/
  
http://www.brightworkcoresearch.com/
+
J5 automated DNA assembly: http://j5.jbei.org/index.php/Main_Page
  
http://portlabpdx.org/wiki/index.php?title=Main_Page
+
Genome Compiler: http://www.genomecompiler.com/
  
http://www.pietervanboheemen.nl/
+
Gibthon: http://django.gibthon.org/
  
http://citizensciencequarterly.com/
 
  
http://www.citizensciencecenter.com/?gclid=CJLtwKXoprcCFczC3god6U4Ahw
+
Transcription and Translation: http://www.attotron.com/cybertory/analysis/trans.htm
  
http://bamh1.com/
+
All-IN-ONE SEQ-ANALYZER: http://www-personal.umich.edu/~ino/blast.html
  
http://diyhpl.us/wiki/diybio/faq/
 
  
http://www.lapaillasse.org
+
GENtle 2: http://ec2-23-20-169-157.compute-1.amazonaws.com/dev/#
  
http://openbioprojects.net/
+
'''DNA oligomer design tools:'''
  
http://hackteria.org/
+
Primer-BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
  
http://blogs.plos.org/citizensci/
+
QuickChange primer design script: http://sosnick.uchicago.edu/stuff/quickchanger.pl
  
http://diybioftw.com/
+
IDT SciTools - oligo design and analysis: http://eu.idtdna.com/scitools/scitools.aspx
  
http://dyibio.org
+
PrimerDigital: http://primerdigital.com/tools/
  
DYI Bio Europe: http://www.diybio.eu/
+
Primer3: http://primer3.wi.mit.edu/
  
http://genefoo.com/
+
Primer3 plus: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
  
Open PCR: http://openpcr.org/
+
InvitroGen OligoPerfect designer: http://tools.invitrogen.com/content.cfm?pageid=9716
  
www.indiebiotech.com
+
PrimerQuest: www.idtdna.com/Scitools/Applications/Primerquest/
  
Ask a Biosafety expert: http://ask.diybio.org/
+
JCVI Primer designer: http://primerdesigner.sourceforge.net/
  
Public Laboratory: http://publiclaboratory.org/home
+
Primer Design Assistant: http://dbb.nhri.org.tw/primer/index.html
  
BOSSLAB: http://bosslab.org/
+
PrimerZ: http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do
  
http://biocurious.org/
+
Primo PCR Primer Design: http://www.changbioscience.com/primo/primo.html
  
http://genspace.org/
+
Eurofins PCR primer design: https://ecom.mwgdna.com/services/webgist/pcr_primer_design_new.tcl?ot=OLIGO_PCRD&item_id=new
  
Science hideout: http://www.youtube.com/user/ScienceHideout
+
Eurofins Sequencing primer design: https://ecom.mwgdna.com/services/manage-primers/design-primer.tcl
  
http://basementbiotech.org/
+
'''DNA/oligomer property calculators:'''
  
http://www.biotinker.com/
+
http://www.basic.northwestern.edu/biotools/oligocalc.html
  
BiologiGaragen: http://biologigaragen.org/
+
'''In silico PCR tools:'''
  
http://haberlandt.blablablab.org/
+
http://exon.ucsc.edu/cgi-bin/hgPcr
  
http://www.bugssonline.org/
+
http://insilico.ehu.es/PCR/
  
Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs
+
http://www.bioinformatics.org/sms2/pcr_products.html
  
http://roningenetics.org/
+
http://qsnp.gen.kyushu-u.ac.jp/genome/InSilicoPCR.html
  
https://www.biotinkering.org/
+
http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold
  
 +
http://www.molbiol-tools.ca/Repeats_secondary_structure_Tm.htm
  
'''Bibliography:'''
+
===Protocols===
  
Process, Not Product: Investigating Recommendations for Improving Citizen Science “Success” : http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064079
+
http://www.protocolpedia.com/
  
 +
OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols
  
===Crowdfunding===
+
Springer Protocols: http://www.springerprotocols.com
  
http://www.petridish.org/
+
Complementary annealing of oligonucleotides: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html
  
https://www.gittip.com/about/
+
Knight lab - annealing protocol: http://openwetware.org/wiki/Knight:Annealing_and_primer_extension_with_Taq_polymerase
  
http://scifundchallenge.org/
+
Knight lab -restriction digest protocol: http://openwetware.org/wiki/Knight:Restriction_Digest
  
http://www.kickstarter.com/
+
Endy: Colony PCR: http://openwetware.org/wiki/Endy:Colony_PCR
  
https://www.microryza.com/
+
Addgene Moleular cloning guide: http://www.addgene.org/plasmid_reference/index/#cloning
  
http://www.indiegogo.com/
+
Addgene restriction digest protocol: http://www.addgene.org/plasmid_protocols/restriction_digest/
  
http://www.gofundme.com/
+
http://www.addgene.org/plasmid_protocols/bacterial_plates/
  
http://www.rockethub.com/
+
http://www.methods.info/Methods/RNA_DNA/restr_analysis.html
  
http://www.scistarter.com/
+
http://www.methodbook.net/dna/restrdig.html
  
Projects:
+
Current Protocols: http://www.currentprotocols.com
  
http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit
+
Science Advisory Board - protocols: http://www.scienceboard.net/resources/protocols.asp?criteria=
  
http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
+
Protocol online: http://protocol-online.org/
  
===Crowdsourced science===
+
http://site.methodological.co/
  
http://www.cellslider.net/
+
http://bio-protocol.org/
  
 +
====Misc. ====
  
===Contract research services===
+
http://www.nature.com/scitable
 +
 
 +
https://www.assaydepot.com/
  
 
https://www.scienceexchange.com/
 
https://www.scienceexchange.com/
  
===Home experiments/projects===
+
http://matt.might.net
  
(Legality may vary depending on your location)
+
http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html
  
How to do a pGlo transformation: http://www.youtube.com/watch?v=sovDqqhQJx8
+
http://www.phdontrack.net/
  
http://www.instructables.com/id/The-Light-Fountain-a-Bioluminescent-Hourglass/
+
Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm
  
 +
J Craig Venter Institute - software: http://www.jcvi.org/cms/research/software/
  
http://cibt.bio.cornell.edu/workshops_and_summer_programs/0608alum/lumos.pdf
+
DNA sequence transformation tools: http://molbiol-tools.ca/Convert.htm
  
http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/%3Eprotocol
+
The Oligator: http://gcat.davidson.edu/igem10/tutorial.html
  
==Art and Strategy==
+
http://www.zappylab.com/apps
  
http://biocouture.co.uk/about/
+
Nucleic Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
  
Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp
+
String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn
  
http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment
+
ProtLifePred protein lifetime calculator: http://protein-n-end-rule.leadhoster.com/
  
http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/
+
See also: http://2012.igem.org/User_talk:Jarlemag and http://2012.igem.org/Team:NTNU_Trondheim/Links
  
http://blog.arduino.cc/2013/05/19/the-mood-lamp-recognizes-your-facial-expressions-and-turns-them-into-light/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer7d04e
+
US National Human Genome Research Institute: http://www.genome.gov/
  
==Personal genomics==
+
Codon table: http://en.wikipedia.org/wiki/DNA_codon_table
  
https://www.23andme.com/
+
LaTeX lab book: http://openwetware.org/wiki/LabbookInLatex
  
http://www.23andyou.com
+
Los Alamos Technical Reports collection: http://www.sciencemadness.org/lanldocs.html
  
http://www.genomesunzipped.org/
+
http://thelabrat.com
  
uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
+
The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home
  
http://www.personalgenomes.org/
+
NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/
  
==Companies==
+
http://www.lablit.com/
  
Evolutionary Solutions: http://www.evosol.co/
 
  
http://www.allelebiotech.com/allele3/index.php
+
Addgene - Genome engineering Guide: https://www.addgene.org/Genome_Engineering/?utm_source=Addgene+March+14%2C+2013+Newsletter+Final&utm_campaign=March+2013+Newsletter&utm_medium=email
  
Era7: http://era7bioinformatics.com/en/index.cfm
+
https://genomeinterpretation.org
  
DNA electronics: http://dnae.co.uk/
+
===Science News & Discussion ===
  
Genome Compiler: http://www.genomecompiler.com/
+
===Magazines/Blogs/Newssites===
  
http://www.strandls.com
+
http://www.labcritics.com/
  
http://www.novozymes.com/en/Pages/default.aspx
+
http://scienceblok.com/
  
http://www.genabler.com
+
http://sciblogs.co.nz/
  
http://www.syntheticgenomics.com/
+
http://www.scicentral.com/index.html
  
BGI: http://www.genomics.cn/en/index
+
http://blogs.discovermagazine.com/seriouslyscience/
  
Gen9: http://gen9bio.com/
+
http://epigenie.com/
  
DNA 2.0: https://www.dna20.com
+
http://www.livescience.com/
  
Integrated DNA Technologies (IDT): http://eu.idtdna.com/site
+
http://scienceblogs.com/
  
GenScript: http://www.genscript.com/
+
http://scientopia.org/blogs/
  
Desktop Genetics: http://www.deskgen.com
+
The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
  
Ginkgo Bioworks: http://ginkgobioworks.com/
+
SciTech Daily: http://scitechdaily.com/
  
Biofab: http://www.biofab.org/
+
The Scientist: http://www.the-scientist.com/
  
http://www.knome.com/
+
GEN Magazine: http://www.genengnews.com/
  
http://www.nucleics.com/
+
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
  
https://www.transcriptic.com/
+
http://www.reportergene.com/
  
Cambrian Genomics:  
+
Super awesome Sylvia: http://sylviashow.com/
https://angel.co/cambrian-genomics
 
http://cambriangenomics.com/
 
  
http://www.genologics.com
+
http://www.technologyreview.com/
  
==Suppliers==
+
http://www.scilogs.com/
  
http://store.p212121.com/
+
'''Blogs:'''
  
http://www.biosciencetools.com/
+
http://ironchefsynbio.wordpress.com/
  
http://www.laboratory-journal.com/
+
http://retractionwatch.wordpress.com/
  
www.labx.com
+
http://www.genomesunzipped.org/
  
http://www.oxfordgenetics.co.uk/
+
http://ing.dk/blogs/folkeforsker
  
BioBasic: http://store.biobasic.com/
+
http://phylogenomics.blogspot.no/
  
Promega: http://no.promega.com/
+
http://88proof.com/synthetic_biology/blog/
  
Qiagen: http://www.qiagen.com/
+
http://bytesizebio.net
  
DongSheng Biotech: http://dongshengbio.com/en/index.asp
+
The hardest science - a psychology blog: http://hardsci.wordpress.com/
  
Macrogen Inc.: http://www.macrogen.com/eng/index/
+
http://dienekes.blogspot.no/
  
Carolina Biological: http://www.carolina.com/
+
Michael Eisen - It's Not Junk: http://www.michaeleisen.org/blog/
  
Epoch Life Sciences: http://www.epochlifescience.com/Default.aspx
+
Open Helix: http://blog.openhelix.eu/
  
http://www.hometrainingtools.com/
+
http://ivory.idyll.org/
  
http://www.labsupplymall.com/
+
http://titojankowski.com/
  
United Nuclear: http://www.unitednuclear.com/
+
See also http://www.microbe.net/microbiology-blogs/
  
New England Biolabs: www.neb.com
+
'''Aggregators:'''
  
Elemental Scientific: http://www.elementalscientific.net/store/Scripts/default.asp
+
http://paper.li/SAGRudd/1323661247
  
Jena BioScience: http://www.jenabioscience.com/
+
http://paper.li/leclercfl/bioscience
  
http://www.synthesisgene.com/
+
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
 +
Norwegian:
  
Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152
+
http://thaliana.blogg.no/1290598240_molekylrbiologi.html
  
http://www.millipore.com/index.do
+
Social & personalized media:
  
See also http://www.made-in-china.com/
+
http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
  
Open Biotechnology: http://www.openbiotech.com/
+
http://trap.it/
  
http://www.metabion.com/home/index.php
 
  
http://bostonbioproducts.com/
+
'''Discussion sites:'''
  
http://www.sbsbio.com/english/dnahc.html
+
http://pubpeer.com/
  
http://www.interfarm.no/produkter/
+
===In the news/Commentaries===
  
http://www.iorodeo.com/
+
George Church - Reading and writing omes: http://www.nature.com/msb/journal/v9/n1/full/msb201275.html
  
'''Used equipment vendors:'''
+
Synthetic Biology comes down to Earth: http://chronicle.com/article/Synthetic-Biology-Comes-Down/137587/
  
http://www.labrecyclers.com/index.html
+
Predictability - the brass ring for synthetic biology: http://newscenter.lbl.gov/science-shorts/2013/03/13/predictability-the-brass-ring-for-synthetic-biology/
  
==Useful links==
+
Press Release - Bootstrapping Biotechnology: Engineers Cooperate to Realize Precision Grammar for Programming Cells http://www.synberc.org/bootstrapping-biotechnology
*[[OpenWetWare:Welcome|Introductory tutorial]]
 
*[[Help|OpenWetWare help pages]]
 
  
 +
HeLa genome sequenced: http://www.embl-hamburg.de/aboutus/communication_outreach/media_relations/2013/130311_Heidelberg/index.html
  
===Conferences and meetings===
+
Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html
  
  
 +
Badomics: http://www.gigasciencejournal.com/content/1/1/6
  
See [[User:Jarle Pahr/Conferences|Conferences]]
+
http://keithbradnam.com/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html
  
===Scientific challenges and competitions===
+
===Jobs===
  
CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/
+
https://www.odesk.com/
  
Assemblathon
+
http://www.tu.no/jobb/
  
Variathon: http://bioinf.dimi.uniud.it/variathon
+
http://www.aftenposten.no/jobb/
  
Alignathon
+
http://www.ingeniorstillinger.no/
  
Sequence squeeze: http://www.sequencesqueeze.org/
+
http://no.indeed.com/jobs?q=Ingeni%C3%B8r&gclid=CJL3_IiL47YCFQdd3godpBMArQ
  
===Resources for researchers===
+
http://www.nature.com/naturejobs/science/jobs
  
http://www.protocol-online.org/science-forums-2/Dissertation-and-Paper-Writing/
+
http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152
  
http://www.protocol-online.org/science-forums-2/Career-Advice/
+
http://yes.jucan.no/
  
https://www.researchgate.net
+
https://uio.easycruit.com/
  
http://friendfeed.com/the-life-scientists
 
  
http://nigerianbioscientist.com/
+
Tips:
  
===Educational resources===
+
Search professional/business search sites for companies in fields of interest.
http://www.bioinformatics.nl/molbi/SimpleCloningLab/index.htm
+
Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.
  
ROSALIND Bioinformatics challenges: http://rosalind.info/problems/locations/
+
===Games===
  
Project Euler: http://projecteuler.net/
+
BioHack: http://marketplace.xbox.com/en-US/Product/BioHack/66acd000-77fe-1000-9115-d802585505ee
  
AddGene molecular biology reference: http://www.addgene.org/mol_bio_reference/
+
http://eterna.cmu.edu/web/
  
https://www.manylabs.org/
+
http://adamilab.msu.edu/evolve-and-conquer/
  
http://www.dnalabbook.co.uk/
+
http://fold.it/portal/
  
=Wiki sites=
+
http://phylo.cs.mcgill.ca/ (publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031362)
  
http://www.scholarpedia.org
+
http://io9.com/these-cool-games-let-you-do-real-life-science-486173006
  
SNPedia.com
+
http://www.citizensort.org/
 
 
http://www.wikigenes.org
 
 
 
http://ecoliwiki.net
 
 
 
===Discussion and communities===
 
 
 
http://molecularbiology.forums.biotechniques.com/
 
 
 
DYI Bio Google Group: https://groups.google.com/forum/?fromgroups#!forum/diybio
 
 
 
http://www.americanbiotechnologist.com/blog/
 
 
 
BioStar - questions and answers on bioinformatics and genomics: http://www.biostars.org/
 
 
 
Biology.stackexchange.com: http://biology.stackexchange.com/
 
 
 
http://www.biology-online.org/
 
 
 
https://www.researchgate.net/
 
 
 
https://www.researchgate.net/topics/?nav=discussions
 
 
 
http://www.protocol-online.org/biology-forums/
 
 
 
Nature Protocols discussion forum: http://network.nature.com/groups/natureprotocols/forum/topics
 
 
 
http://www.reddit.com/r/labrats/
 
 
 
http://scienceboard.net/forum/default.asp
 
 
 
http://branch.com/g/level-headed-biotech
 
 
 
http://www.bio.net/
 
 
 
===Apps===
 
 
 
mPartsregistry: http://mpartsregistry.appspot.com
 
 
 
===Persons/Research groups===
 
 
 
http://genefish.wikispaces.com/
 
 
 
Mark Pallen: http://www2.warwick.ac.uk/fac/med/research/microinfect/staff/pallengroup/
 
 
 
Chris Anderson lab: https://andersonlab.qb3.berkeley.edu/
 
 
 
Magni Paolo: http://www.labmedinfo.org/people/magni
 
 
 
http://www.rpgroup.caltech.edu/publications/
 
 
 
Heng Li. "Alignment God".
 
 
 
Dworkin lab: https://www.msu.edu/~idworkin/publications.html
 
 
 
Titus Brown:
 
 
 
Erlich lab: http://erlichlab.wi.mit.edu/index.html
 
 
 
Cristopher mason: http://www.masonlab.net/
 
 
 
http://openwetware.org/wiki/User:Vincent
 
 
 
Markus Gershater
 
 
 
http://www.princeton.edu/~ajlgroup/
 
 
 
Heng Li
 
 
 
Michael Cashel: https://science.nichd.nih.gov/confluence/display/pgd/Michael+Cashel+Lab
 
 
 
Jim Collins: http://www.bu.edu/abl/
 
 
 
Jason Kelly: http://openwetware.org/wiki/Jason_Kelly
 
 
 
Tom Ellis: http://openwetware.org/wiki/User:Ellis
 
 
 
George Church: http://arep.med.harvard.edu/gmc/
 
 
 
Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html
 
 
 
Chris Voigt
 
 
 
Bernahrd Ø Pallsson: http://gcrg.ucsd.edu/Researchers/Palsson
 
 
 
Tom Knight
 
 
 
Joe Felsenstein: http://www.gs.washington.edu/faculty/felsenstein.htm
 
*Professor of Genome Sciences and Biology, University of Washington.
 
 
 
Drew Endy: http://openwetware.org/wiki/User:Endy
 
 
 
Densmore lab: http://people.bu.edu/dougd/research.html
 
 
 
Ron Weiss: http://groups.csail.mit.edu/synbio/people/professor-ron-weiss/
 
 
 
Jean Peccoud
 
 
 
Jonathan Eisen
 
 
 
Martin Fusenegger
 
 
 
Pamela Silver
 
 
 
Rob Carlson
 
 
 
Ethan Perlstein: http://www.perlsteinlab.com/
 
 
 
Anthony Evans
 
 
 
Nick Loman:
 
 
 
http://pathogenomics.bham.ac.uk/clinicogenomics/
 
 
 
http://pathogenomics.bham.ac.uk/blog/author/nick/
 
 
 
Titus Brown: http://ivory.idyll.org/blog/category/science.html
 
 
 
Lex Nedebragt:
 
 
 
http://contig.wordpress.com/
 
 
 
https://twitter.com/lexnederbragt
 
 
 
Manual Corpas:
 
 
 
Barry L Wanner: https://www.bio.purdue.edu/molecular_biosciences/directory.php?refID=30
 
*Made many E. coli strains.
 
 
 
Andrew Hessel: http://andrewhessel.com/
 
 
 
===Societies and associations===
 
 
 
Society for applied microbiology: http://www.sfam.org.uk/
 
 
 
American Association for Clinical Chemistry : http://www.aacc.org/Pages/default.aspx
 
 
 
Royal Society of Chemistry: http://www.rsc.org/
 
 
 
Society for general microbiology: http://www.sgm.ac.uk/
 
 
 
American society for microbiology: http://www.asm.org/
 
 
 
Norsk Kjemisk selskap: http://www.kjemi.no/
 
 
 
International Society for Systems Biology: http://www.issb.org/
 
 
 
Genetics Society of America: http://www.genetics-gsa.org/
 
 
 
British Society for Gene and Cell Therapy: https://www.facebook.com/BSGCT
 
 
 
American Society of Human Genetics (ASHG):
 
 
 
Society for Molecular Biology and Evolution (SMBE): http://www.smbe.org/
 
 
 
===Publications===
 
 
 
 
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
! Journal name!! Publisher !! Open access status !! Link
 
|-
 
| ACS Synthetic Biology || American Chemical Society ||No ||  http://pubs.acs.org/journal/asbcd6
 
|-
 
| Bioengineered (Previously: Bioengineered bugs) || Landes Bioscience ||Partial ||http://dev.landesbioscience.com/journals/bioe/
 
|-
 
|Bioinformatics||Oxford Journals|| ||http://bioinformatics.oxfordjournals.org/
 
|-
 
|Biology Open||Company of Biologists||Yes||http://bio.biologists.org/
 
|-
 
|BMC Medical Genomics||BMC||Yes||http://www.biomedcentral.com/bmcmedgenomics/
 
|-
 
|BMC Proceedings||BMC||Yes||http://www.biomedcentral.com/bmcproc
 
|-
 
| PLOS One  ||Public Library of Science || Yes ||http://www.plosone.org/
 
|-
 
| Nucleic Acids Research|| Oxford Journals || Yes || http://nar.oxfordjournals.org/
 
|-
 
|BMC Systems Biology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcsystbiol/
 
|-
 
|BMC Microbiology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcmicrobiol
 
|-
 
|Cell||Cell Press|| ||http://www.cell.com/
 
|-
 
|Cell Reports||Cell Press ||Yes||http://cellreports.cell.com/
 
|-
 
|The EMBO Journal||Nature Publishing Group ||No||http://www.nature.com/emboj/index.html
 
|-
 
|Frontiers in Synthetic Biology||Nature Publishing Group|| ||http://www.frontiersin.org/Synthetic_Biology/about
 
|-
 
|Genetics||Genetics Society of America|| ||http://www.genetics.org/
 
|-
 
|G3: Genes, Genomes, Genetics Mission ||Genetics Society of America|| ||http://www.g3journal.org/
 
|-
 
|Genome Research||Cold Spring Harbor Press||Partial (6 month embargo)|| http://genome.cshlp.org/
 
|-
 
|Genome Biology||BMC||Yes||http://genomebiology.com/
 
|-
 
|Genome Medicine||BioMedCentral||Yes||http://genomemedicine.com/
 
|-
 
|Journal of Experimental Biology||Company of Biologists||http://jeb.biologists.org/
 
|-
 
|Journal of molecular biology||Elsevier ||Partial||http://www.journals.elsevier.com/journal-of-molecular-biology/
 
|-
 
|Journal of biological chemistry||American Society for Biochemistry and Molecular Biology.  ||No||http://www.jbc.org/
 
|-
 
|Journal of bacteriology||American Society for Microbiology ||No||http://jb.asm.org/
 
|-
 
|Journal of Bioscience and Engineering||  || ||http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
 
|-
 
|Journal of clinical microbiology||American Society for Microbiology||No||http://jcm.asm.org/
 
|-
 
|mBio||ASM||Yes||http://mbio.asm.org/
 
|-
 
|Methods||Elsevier||No||http://www.journals.elsevier.com/methods
 
|-
 
|Microbiology||SGM/HighWire Press||No||http://mic.sgmjournals.org/
 
|-
 
|Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology Reviews||ASM|| ||mmbr.asm.org
 
|-
 
|Metabolic Engineering||Elsevier||Partial||http://www.journals.elsevier.com/metabolic-engineering/
 
|-
 
|Molecular Systems Biology||EMBO/Nature Publishing Group||Yes||http://www.nature.com/msb/index.html||
 
|-
 
|PLOS Computational Biology||Public Library of Science||Yes||http://www.ploscompbiol.org/
 
|-
 
|PLOS Pathogens||PLOS||Yes||http://www.plospathogens.org/
 
|-
 
|Proceedings of the National Academy of Sciences||National Academy of Sciences||No||http://www.pnas.org/
 
|-
 
|Protein expression and purification||Elsevier||No||http://www.sciencedirect.com/science/journal/10465928
 
|-
 
|Genome Announcements||ASM||Yes||http://genomea.asm.org/
 
|-
 
|Futures||Elsevier||?||http://www.sciencedirect.com/science/journal/00163287
 
|-
 
|Microbial Cell Factories||BioMedCentral||Yes||http://www.microbialcellfactories.com/
 
|-
 
|Engineering Studies||Taylor & Francis|| ?||http://www.tandfonline.com/loi/test20
 
|-
 
|FEMS Microbiology Reviews|| || ||http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
 
|-
 
|Nature Biotechnology||Nature Publishing Group||No||http://www.nature.com/nbt/index.html
 
|-
 
|Nature Genetics||Nature Publishing group||No||http://www.nature.com/ng/index.html
 
|-
 
|Plasmid||Elsevier||No||http://www.journals.elsevier.com/plasmid/
 
|-
 
|Journal of Computational Biology||Liebert Publishing||No||http://www.liebertpub.com/CMB
 
|-
 
|Trends in Biochemical Sciences||Elsevier|| ||http://www.sciencedirect.com/science/journal/09680004
 
|-
 
|Trends in Microbiology||Elsevier/Cell Press|| ||http://www.sciencedirect.com/science/journal/0966842X
 
|-
 
|Molecular Genetics & Genomic Medicine||Wiley||Yes||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
 
|-
 
|Molecular genetics and genomics||Springer Verlag|| ||http://link.springer.com/journal/438
 
|-
 
|Biochemistry and Molecular Biology Education||Wiley||No||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
 
|-
 
|Current opinion in chemical biology||Elsevier|| ||http://www.sciencedirect.com/science/journal/13675931
 
|-
 
|New England Journal of Medicine||NEJM Group|| ||http://www.nejm.org/
 
|-
 
|Systems and Synthetic Biology||Springer|| ||http://link.springer.com/journal/11693
 
|-
 
|Scientific Reports||Nature Publishing Group||Yes||http://www.nature.com/srep/index.html
 
|}
 
 
 
 
 
Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/
 
 
 
Computational and Structural Biotechnology Journal
 
 
 
 
 
http://www.journalnetwork.org/journals/science-general/citizen-science/citizen-science-innovation.html
 
 
 
Biotechniques: http://www.biotechniques.com/
 
 
 
https://www.openlibhums.org/
 
 
 
Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727
 
 
 
http://www.g3journal.org/
 
 
 
http://push.cwcon.org/
 
 
 
eLife: http://elife.elifesciences.org/
 
 
 
https://peerj.com/
 
 
 
Faculty of 1000: http://f1000.com/
 
 
 
 
 
Social Science Research Network: http://www.ssrn.com/
 
 
 
 
 
Open access:
 
 
 
http://en.wikipedia.org/wiki/List_of_open-access_journals
 
 
 
http://scholarlyoa.com/
 
 
 
http://www.doaj.org/
 
 
 
http://www.opendoar.org/
 
 
 
http://blogs.scientificamerican.com/guest-blog/2013/04/03/who-killed-the-preprint-and-could-it-make-a-return/
 
 
 
Publication tools:
 
 
 
https://collage.elsevier.com/
 
 
 
Reference management / Social bookmarking:
 
 
 
http://www.mendeley.com/
 
 
 
http://www.citeulike.org/
 
 
 
JabRef reference manager: http://jabref.sourceforge.net/
 
 
 
===Publishers===
 
 
 
Springer
 
 
 
Elsevier
 
 
 
CRC Press
 
 
 
Horizon Press
 
 
 
===Databases/Repositories===
 
 
 
PlasmID database: http://plasmid.med.harvard.edu/PLASMID/
 
 
 
Addgene plasmid repository: http://www.addgene.org/
 
 
 
DNASU plasid repository: http://dnasu.asu.edu/DNASU/
 
 
 
The Open Construct Database: http://www.the-odin.com
 
 
 
Bionumbers - [http://bionumbers.hms.harvard.edu/default.aspx The database of useful biological numbers]
 
 
 
EcoCyc - E. coli K-12 MG1655 database: http://www.ecocyc.org/
 
 
 
EcoGene: http://www.ecogene.org
 
 
 
JWS Online model database: http://jjj.biochem.sun.ac.za/database/
 
 
 
http://systems-biology.org/resources/model-repositories/
 
 
 
Genome-Scale metabolic network database: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm
 
 
 
Array express: http://www.ebi.ac.uk/arrayexpress/
 
 
 
Rebase restriction enzyme database: http://rebase.neb.com/rebase/rebase.html
 
 
 
1000 genomes project: http://browser.1000genomes.org/index.html
 
 
 
BRENDA Enzymes: http://www.brenda-enzymes.info/
 
 
 
KEGG
 
 
 
GenBank
 
 
 
http://datadryad.org/
 
 
 
http://www.cathdb.info/
 
 
 
===Codon usage===
 
 
 
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333
 
 
 
Codon usage analyzer: http://www.bioinformatics.org/sms2/codon_usage.html
 
 
 
===Other informational resources===
 
 
 
National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html
 
 
 
http://seqanswers.com
 
 
 
NCBI vs EMBL vs DDBJ.: http://lib.bioinfo.pl/courses/view/151
 
 
 
The DDBJ/EMBL/GenBank Feature Table Definition: http://www.insdc.org/files/feature_table.html#1
 
 
 
http://openwetware.org/wiki/DNA - Contains many protocols
 
 
 
Bite Size Bio: http://bitesizebio.com/
 
 
 
BenchFly: http://www.benchfly.com/
 
 
 
http://biologicalworld.com/protocols.htm
 
 
 
http://www.methods.info/
 
 
 
http://www.biotechdaily.com/
 
 
 
http://www.zenbiology.com/
 
 
 
http://www.my-whiteboard.com/
 
 
 
http://lablife.org
 
 
 
http://www.molbiol-tools.ca/
 
 
 
http://www.molecularinfo.com/MTM/MTM.html
 
 
 
http://www.openhelix.com/ - Genomics and bioinformatics resources.
 
 
 
===Programming===
 
 
 
BioPython: http://biopython.org/wiki/Main_Page
 
 
 
CodEval -  programming challenges: http://codeeval.com/
 
 
 
===Law and ethics===
 
 
 
http://www.genomicslawreport.com/
 
 
 
American journal of Bioethics: http://www.tandfonline.com/toc/uajb20/current
 
 
 
IASB Code of Conduct for best practices in gene synthesis: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/code-of-conduct-for-best-practices-in-gene-synthesis/
 
 
 
IASB - About Biosafety & Security: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/biosafety-biosecurity/
 
 
 
Andrew W Torrance on DNA copyright: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2017670
 
 
 
 
 
===Cloning===
 
 
 
SLIC, Gibson, CPEC and SLiCE assembly methods: http://j5.jbei.org/j5manual/pages/22.html
 
 
 
RF cloning: http://www.rf-cloning.org/QandA.php
 
 
 
PCR Primer design: http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm
 
 
 
PCR: http://www.molbiol-tools.ca/PCR.htm
 
 
 
OpenWetWare - designing primers: http://openwetware.org/wiki/Designing_primers
 
 
 
PCR Guide: http://medicine.yale.edu/labs/henegariu/www/tavi/Guide.html
 
 
 
PCR troubleshooting: http://medicine.yale.edu/labs/henegariu/www/tavi/Trblesht.html
 
 
 
DNA Tm estimation methods: http://openwetware.org/wiki/Primer_Tm_estimation_methods
 
 
 
DNA stability: http://openwetware.org/wiki/DNA_stability
 
 
 
E. coli cloning checklist: http://openwetware.org/wiki/Cloning_Checklist
 
 
 
Guide to Gibson assembly: http://www.synbio.org.uk/dna-assembly/guidetogibsonassembly.html
 
 
 
Primer design guidelines: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
 
 
 
===Sequencing===
 
 
 
Design of sequencing primers: http://seqcore.brcf.med.umich.edu/doc/dnaseq/primers.html
 
 
 
Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi: http://biology.duke.edu/fungi/mycolab/primers.htm
 
 
 
GenScript DNA Sequencing Primers Design Tool: http://www.genscript.com/cgi-bin/tools/sequencing_primer_design
 
 
 
===Software tools===
 
 
 
Molecular Biology Freeware for Windows: http://molbiol-tools.ca/molecular_biology_freeware.htm#Graphic%20packages
 
 
 
Molecular Biology & Bioinformatics Resources: http://library.weill.cornell.edu/eresources/molbio.html
 
 
 
Bioinformatics Tools and Resources for Biomedical Scientists and Students - http://www.changbioscience.com/virtualab.html
 
 
 
 
 
DNA copy number calculator: http://www.uri.edu/research/gsc/resources/cndna.html
 
 
 
Graphics software:
 
 
 
===Systems Biology===
 
 
 
http://systems-biology.org/
 
 
 
Cytoscape: www.cytoscape.org
 
 
 
CAIN stochastic simulations for chemical kinetics: http://cain.sourceforge.net/
 
 
 
COBRA Constraints-based modelling toolbox:
 
 
 
CellNetAnalyzer: http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html
 
 
 
CellDesigner: http://celldesigner.org/
 
 
 
OptFlux: http://www.optflux.org/
 
 
 
Systems Biology Markup Language: www.sbml.org
 
 
 
SBML to LaTex report generator: http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/index.html
 
 
 
Systems Biology Toolbox 2 for MATLAB: http://www.sbtoolbox2.org/main.php
 
 
 
http://www.sysbio.de/
 
 
 
Handbook of Systems Biology: http://www.sciencedirect.com/science/book/9780123859440
 
 
 
Reflexive Systems Biology: http://portal.cbu.uib.no/rsb
 
 
 
===Bioinformatics & Annotation===
 
 
 
Neural Network Promoter Prediction: http://www.fruitfly.org/seq_tools/promoter.html
 
 
 
Artemis genome browser: http://www.sanger.ac.uk/resources/software/artemis/
 
 
 
BASYS Bacterial Annotation software: http://basys.ca/
 
 
 
SoftBerry: http://linux1.softberry.com/berry.phtml
 
 
 
Promethease: http://snpedia.com/index.php/Promethease
 
 
 
GLIMMER microbial gene-finding system: http://www.cbcb.umd.edu/software/glimmer/
 
 
 
Promoter & termination site search tools: http://molbiol-tools.ca/Promoters.htm
 
 
 
Phyre 2 - protein fold recognition: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
 
 
 
FITBAR DNA binding protein binding site predictor: http://archaea.u-psud.fr/fitbar/
 
 
 
Simple Consensus Maker: http://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html
 
 
 
Model SEED - blog: http://blog.theseed.org/model_seed/
 
 
 
Model SEED - Viewer: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView
 
 
 
http://www.bioinformatics.org/
 
 
 
Plasmid map drawer: http://www.rf-cloning.org/savvy.php
 
 
 
EMBOSS ((European Molecular Biology Open Software Suite): http://bips.u-strasbg.fr/EMBOSS/
 
 
 
BioBrick -> GenBank converter: http://2010.igem.org/Team:Cambridge/Tools/GenBank
 
 
 
 
 
HMMER: http://hmmer.janelia.org/
 
 
 
Jcat Codon Adaption Tool: http://www.jcat.de/
 
 
 
===Cloning & Construction===
 
 
 
The Constructor: http://2011.igem.org/Team:Wageningen_UR/Softwaretool/
 
 
 
NEBcutter: http://tools.neb.com/NEBcutter2/
 
 
 
J5 automated DNA assembly: http://j5.jbei.org/index.php/Main_Page
 
 
 
Genome Compiler: http://www.genomecompiler.com/
 
 
 
Gibthon: http://django.gibthon.org/
 
 
 
 
 
Transcription and Translation: http://www.attotron.com/cybertory/analysis/trans.htm
 
 
 
All-IN-ONE SEQ-ANALYZER: http://www-personal.umich.edu/~ino/blast.html
 
 
 
 
 
GENtle 2: http://ec2-23-20-169-157.compute-1.amazonaws.com/dev/#
 
 
 
'''DNA oligomer design tools:'''
 
 
 
Primer-BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
 
 
 
QuickChange primer design script: http://sosnick.uchicago.edu/stuff/quickchanger.pl
 
 
 
IDT SciTools - oligo design and analysis: http://eu.idtdna.com/scitools/scitools.aspx
 
 
 
PrimerDigital: http://primerdigital.com/tools/
 
 
 
Primer3: http://primer3.wi.mit.edu/
 
 
 
Primer3 plus: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
 
 
 
InvitroGen OligoPerfect designer: http://tools.invitrogen.com/content.cfm?pageid=9716
 
 
 
PrimerQuest: www.idtdna.com/Scitools/Applications/Primerquest/
 
 
 
JCVI Primer designer: http://primerdesigner.sourceforge.net/
 
 
 
Primer Design Assistant: http://dbb.nhri.org.tw/primer/index.html
 
 
 
PrimerZ: http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do
 
 
 
Primo PCR Primer Design: http://www.changbioscience.com/primo/primo.html
 
 
 
Eurofins PCR primer design: https://ecom.mwgdna.com/services/webgist/pcr_primer_design_new.tcl?ot=OLIGO_PCRD&item_id=new
 
 
 
Eurofins Sequencing primer design: https://ecom.mwgdna.com/services/manage-primers/design-primer.tcl
 
 
 
'''DNA/oligomer property calculators:'''
 
 
 
http://www.basic.northwestern.edu/biotools/oligocalc.html
 
 
 
'''In silico PCR tools:'''
 
 
 
http://exon.ucsc.edu/cgi-bin/hgPcr
 
 
 
http://insilico.ehu.es/PCR/
 
 
 
http://www.bioinformatics.org/sms2/pcr_products.html
 
 
 
http://qsnp.gen.kyushu-u.ac.jp/genome/InSilicoPCR.html
 
 
 
http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold
 
 
 
http://www.molbiol-tools.ca/Repeats_secondary_structure_Tm.htm
 
 
 
===Protocols===
 
 
 
http://www.protocolpedia.com/
 
 
 
OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols
 
 
 
Springer Protocols: http://www.springerprotocols.com
 
 
 
Complementary annealing of oligonucleotides: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html
 
 
 
Knight lab - annealing protocol: http://openwetware.org/wiki/Knight:Annealing_and_primer_extension_with_Taq_polymerase
 
 
 
Knight lab -restriction digest protocol: http://openwetware.org/wiki/Knight:Restriction_Digest
 
 
 
Endy: Colony PCR: http://openwetware.org/wiki/Endy:Colony_PCR
 
 
 
Addgene Moleular cloning guide: http://www.addgene.org/plasmid_reference/index/#cloning
 
 
 
Addgene restriction digest protocol: http://www.addgene.org/plasmid_protocols/restriction_digest/
 
 
 
http://www.addgene.org/plasmid_protocols/bacterial_plates/
 
 
 
http://www.methods.info/Methods/RNA_DNA/restr_analysis.html
 
 
 
http://www.methodbook.net/dna/restrdig.html
 
 
 
Current Protocols: http://www.currentprotocols.com
 
 
 
Science Advisory Board - protocols: http://www.scienceboard.net/resources/protocols.asp?criteria=
 
 
 
Protocol online: http://protocol-online.org/
 
 
 
http://site.methodological.co/
 
 
 
http://bio-protocol.org/
 
 
 
====Misc. ====
 
 
 
http://www.nature.com/scitable
 
 
 
https://www.assaydepot.com/
 
 
 
https://www.scienceexchange.com/
 
 
 
http://matt.might.net
 
 
 
http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html
 
 
 
http://www.phdontrack.net/
 
 
 
Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm
 
 
 
J Craig Venter Institute - software: http://www.jcvi.org/cms/research/software/
 
 
 
DNA sequence transformation tools: http://molbiol-tools.ca/Convert.htm
 
 
 
The Oligator: http://gcat.davidson.edu/igem10/tutorial.html
 
 
 
http://www.zappylab.com/apps
 
 
 
Nucleic Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
 
 
 
String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn
 
 
 
ProtLifePred protein lifetime calculator: http://protein-n-end-rule.leadhoster.com/
 
 
 
See also: http://2012.igem.org/User_talk:Jarlemag and http://2012.igem.org/Team:NTNU_Trondheim/Links
 
 
 
US National Human Genome Research Institute: http://www.genome.gov/
 
 
 
Codon table: http://en.wikipedia.org/wiki/DNA_codon_table
 
 
 
LaTeX lab book: http://openwetware.org/wiki/LabbookInLatex
 
 
 
Los Alamos Technical Reports collection: http://www.sciencemadness.org/lanldocs.html
 
 
 
http://thelabrat.com
 
 
 
The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home
 
 
 
NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/
 
 
 
http://www.lablit.com/
 
 
 
 
 
Addgene - Genome engineering Guide: https://www.addgene.org/Genome_Engineering/?utm_source=Addgene+March+14%2C+2013+Newsletter+Final&utm_campaign=March+2013+Newsletter&utm_medium=email
 
 
 
https://genomeinterpretation.org
 
 
 
===Science News & Discussion ===
 
 
 
===Magazines/Blogs/Newssites===
 
 
 
http://scienceblok.com/
 
 
 
http://sciblogs.co.nz/
 
 
 
http://www.scicentral.com/index.html
 
 
 
http://blogs.discovermagazine.com/seriouslyscience/
 
 
 
http://epigenie.com/
 
 
 
http://www.livescience.com/
 
 
 
http://scienceblogs.com/
 
 
 
http://scientopia.org/blogs/
 
 
 
The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
 
 
 
SciTech Daily: http://scitechdaily.com/
 
 
 
The Scientist: http://www.the-scientist.com/
 
 
 
GEN Magazine: http://www.genengnews.com/
 
 
 
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
 
 
 
http://www.reportergene.com/
 
 
 
Super awesome Sylvia: http://sylviashow.com/
 
 
 
http://www.technologyreview.com/
 
 
 
http://www.scilogs.com/
 
 
 
'''Blogs:'''
 
 
 
http://ironchefsynbio.wordpress.com/
 
 
 
http://retractionwatch.wordpress.com/
 
 
 
http://www.genomesunzipped.org/
 
 
 
http://ing.dk/blogs/folkeforsker
 
 
 
http://phylogenomics.blogspot.no/
 
 
 
http://88proof.com/synthetic_biology/blog/
 
 
 
http://bytesizebio.net
 
 
 
The hardest science - a psychology blog: http://hardsci.wordpress.com/
 
 
 
http://dienekes.blogspot.no/
 
 
 
Michael Eisen - It's Not Junk: http://www.michaeleisen.org/blog/
 
 
 
Open Helix: http://blog.openhelix.eu/
 
 
 
http://ivory.idyll.org/
 
 
 
http://titojankowski.com/
 
 
 
See also http://www.microbe.net/microbiology-blogs/
 
 
 
'''Aggregators:'''
 
 
 
http://paper.li/SAGRudd/1323661247
 
 
 
http://paper.li/leclercfl/bioscience
 
 
 
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
 
Norwegian:
 
 
 
http://thaliana.blogg.no/1290598240_molekylrbiologi.html
 
 
 
Social & personalized media:
 
 
 
http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
 
 
 
http://trap.it/
 
 
 
 
 
'''Discussion sites:'''
 
 
 
http://pubpeer.com/
 
 
 
===In the news/Commentaries===
 
 
 
George Church - Reading and writing omes: http://www.nature.com/msb/journal/v9/n1/full/msb201275.html
 
 
 
Synthetic Biology comes down to Earth: http://chronicle.com/article/Synthetic-Biology-Comes-Down/137587/
 
 
 
Predictability - the brass ring for synthetic biology: http://newscenter.lbl.gov/science-shorts/2013/03/13/predictability-the-brass-ring-for-synthetic-biology/
 
 
 
Press Release - Bootstrapping Biotechnology: Engineers Cooperate to Realize Precision Grammar for Programming Cells http://www.synberc.org/bootstrapping-biotechnology
 
 
 
HeLa genome sequenced: http://www.embl-hamburg.de/aboutus/communication_outreach/media_relations/2013/130311_Heidelberg/index.html
 
 
 
Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html
 
 
 
 
 
Badomics: http://www.gigasciencejournal.com/content/1/1/6
 
 
 
http://keithbradnam.com/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html
 
 
 
===Jobs===
 
 
 
https://www.odesk.com/
 
 
 
http://www.tu.no/jobb/
 
 
 
http://www.aftenposten.no/jobb/
 
 
 
http://www.ingeniorstillinger.no/
 
 
 
http://no.indeed.com/jobs?q=Ingeni%C3%B8r&gclid=CJL3_IiL47YCFQdd3godpBMArQ
 
 
 
http://www.nature.com/naturejobs/science/jobs
 
 
 
http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152
 
 
 
http://yes.jucan.no/
 
 
 
https://uio.easycruit.com/
 
 
 
 
 
Tips:
 
 
 
Search professional/business search sites for companies in fields of interest.
 
Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.
 
 
 
===Games===
 
 
 
BioHack: http://marketplace.xbox.com/en-US/Product/BioHack/66acd000-77fe-1000-9115-d802585505ee
 
 
 
http://eterna.cmu.edu/web/
 
  
http://adamilab.msu.edu/evolve-and-conquer/
+
http://sourceforge.net/projects/brainworkshop/?source=directory
 
 
http://fold.it/portal/
 
 
 
http://phylo.cs.mcgill.ca/ (publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031362)
 
 
 
http://io9.com/these-cool-games-let-you-do-real-life-science-486173006
 
 
 
http://www.citizensort.org/
 
  
 
===Just for Fun===
 
===Just for Fun===

Revision as of 04:15, 17 August 2013

Contact Info

Jarle Pahr
  • Jarle Pahr
  • Norwegian University of Science and Technology

jarlemag@stud.ntnu.no

Education

2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology


Notes

See Notes

Projects

ppGpp MSc. project

Organisms

See Organisms

Interesting articles

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Environmentally controlled invasion of cancer cells by engineered bacteria

Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Genetic programs constructed from layered logic gates in single cells

Research centres/labs

Wyss institute: http://wyss.harvard.edu/

Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/

Cold Spring Harbor Laboratory: http://www.cshl.edu/

Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/

Insititute for Systems Biology: https://www.systemsbiology.org

Virginia Bioinformatics Institute: https://www.vbi.vt.edu/

European Bioinformatics Institute: http://www.ebi.ac.uk/

ATCC: http://www.lgcstandards-atcc.org/

European Molecular Biology Laboratory (EMBL): http://www.embl.de/

http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html


http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/

http://korflab.ucdavis.edu/

Research programs/projects

Statseq: http://www2.ab.wur.nl/statseq/

Online learning

https://www.coursera.org/course/usefulgenetics

http://www.skillshare.com/

Portals:

Saylor: http://www.saylor.org/majors/biology/

http://www.class-central.com/

http://www.core.org.cn

https://www.coursera.org/

MIT Open Courseware: http://ocw.mit.edu/index.htm

Udacity:https://www.udacity.com/

EdX: https://www.edx.org/courses

Khan academy: https://www.khanacademy.org

http://www.bioinformatics.org/edu/course/

Specific courses:

Computational investing course: https://www.coursera.org/course/compinvesting1

Linear and discrete optimization course: https://www.coursera.org/course/linearopt

https://www.coursera.org/course/macroeconomics

Bioinformatics algorithms: https://www.coursera.org/course/bioinformatics

Financial Engineering: https://www.coursera.org/course/fe

A beginner's guide to irrational behavior: https://www.coursera.org/course/behavioralecon

Computational molecular evolution: https://www.coursera.org/course/molevol

https://www.coursera.org/course/netsysbio

Introduction to Systems Biology: https://www.coursera.org/course/sysbio

Biostatistics bootcamp: https://www.coursera.org/course/biostats

High performance scientific computing: https://www.coursera.org/course/scicomp

Language

Chinese

http://english.cntv.cn/learnchinese/

http://popupchinese.com/

http://www.sinosplice.com/

http://www.clearchinese.com/learn-chinese

http://www.instantspeakchinese.com/

"The 5 stages of learning chinese:" http://www.sinosplice.com/learn-chinese/stages-to-learning-chinese

Courses:

http://www.languageinfusion.no/kinesiskonline.php?gclid=CNfCsP_N3LYCFc5a3godPh0ATQ

http://www.learn-mandarin-help.com/software-to-learn-chinese.html

http://www.rocketlanguages.com/chinese/premium/index.php?hop=jon1573

http://chinesepod.com/

http://www.sinosplice.com/learn-chinese/an-insiders-look-at-chinesepod

http://store.instantimmersion.com/chinese.html

http://www.fluenz.com/languages/mandarin/learn-mandarin/

http://www.pimsleur.com/learn-mandarin-chinese

http://www.learn-mandarin-help.com/rosetta-stone-mandarin.html

http://www.amazon.com/Rosetta-Stone-Chinese-Mandarin-Level/dp/1608299643

http://www.rosettastone.eu/lp/brand/?cid=se-ggeu1b13&rd=0

http://www.learn-mandarin-help.com/

http://www.fsi-language-courses.org/Content.php

Foreign Service Institute language courses - Standard Chinese, a modular approach: http://www.fsi-language-courses.org/Content.php?page=Chinese

http://ocw.mit.edu/courses/foreign-languages-and-literatures/21f-101-chinese-i-regular-spring-2006/


Books:


http://www.amazon.com/gp/product/7800521346/ref=cm_cr_asin_lnk

New Practical Chinese Reader Textbook 1: http://www.amazon.com/New-Practical-Chinese-Reader-Textbook/dp/7561910401

New Practical Chinese Reader series: http://www.sinoliterature.co.uk/english/index.aspx?category=68&gclid=CO2pyuLB3LYCFcNQ3god_CgAHg

Reading/Writing:

http://www.amazon.com/Reading-Writing-Chinese-Simplified-Character/dp/0804835098/ref=cm_cr-mr-title

http://www.quickmandarin.com/chinesepinyintable/

Dictionaries:

http://www.nciku.com/

http://www.zhongwen.com/


Speaking:

SpeakGoodChinese: http://www.speakgoodchinese.org/

Synthetic Biology

See Synthetic Biology

Biological part collections

http://partsregistry.org

https://biobricks.org/bpa/find-a-part/

https://registry.synberc.org/

https://public-registry.jbei.org/ (http://www.ncbi.nlm.nih.gov/pubmed/22718978)

DIY Bio/Citizen science

See DIY Bio

http://citizensciencequarterly.com/

Art and Strategy

http://biocouture.co.uk/about/

Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp

http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment

http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/

http://blog.arduino.cc/2013/05/19/the-mood-lamp-recognizes-your-facial-expressions-and-turns-them-into-light/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer7d04e

http://thefinchandpea.com/2010/06/20/what-the-end-of-the-world-says-about-science/

http://thefinchandpea.com/2013/08/04/sunday-poem-lord-byrons-post-apocalyptic-vision/

Personal genomics

https://www.23andme.com/

http://www.23andyou.com

http://www.genomesunzipped.org/

uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome

http://www.personalgenomes.org/

Companies

Evolutionary Solutions: http://www.evosol.co/

http://www.allelebiotech.com/allele3/index.php

Era7: http://era7bioinformatics.com/en/index.cfm

DNA electronics: http://dnae.co.uk/

Genome Compiler: http://www.genomecompiler.com/

http://www.strandls.com

http://www.novozymes.com/en/Pages/default.aspx

http://www.genabler.com

http://www.syntheticgenomics.com/

BGI: http://www.genomics.cn/en/index

Gen9: http://gen9bio.com/

DNA 2.0: https://www.dna20.com

Integrated DNA Technologies (IDT): http://eu.idtdna.com/site

GenScript: http://www.genscript.com/

Desktop Genetics: http://www.deskgen.com

Ginkgo Bioworks: http://ginkgobioworks.com/

Biofab: http://www.biofab.org/

http://www.knome.com/

http://www.nucleics.com/

https://www.transcriptic.com/

Cambrian Genomics: https://angel.co/cambrian-genomics http://cambriangenomics.com/

http://www.genologics.com

Suppliers

http://store.p212121.com/

http://www.biosciencetools.com/

http://www.laboratory-journal.com/

www.labx.com

http://www.oxfordgenetics.co.uk/

BioBasic: http://store.biobasic.com/

Promega: http://no.promega.com/

Qiagen: http://www.qiagen.com/

DongSheng Biotech: http://dongshengbio.com/en/index.asp

Macrogen Inc.: http://www.macrogen.com/eng/index/

Carolina Biological: http://www.carolina.com/

Epoch Life Sciences: http://www.epochlifescience.com/Default.aspx

http://www.hometrainingtools.com/

http://www.labsupplymall.com/

United Nuclear: http://www.unitednuclear.com/

New England Biolabs: www.neb.com

Elemental Scientific: http://www.elementalscientific.net/store/Scripts/default.asp

Jena BioScience: http://www.jenabioscience.com/

http://www.synthesisgene.com/

Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152

http://www.millipore.com/index.do

See also http://www.made-in-china.com/

Open Biotechnology: http://www.openbiotech.com/

http://www.metabion.com/home/index.php

http://bostonbioproducts.com/

http://www.sbsbio.com/english/dnahc.html

http://www.interfarm.no/produkter/

http://www.iorodeo.com/

Used equipment vendors:

http://www.labrecyclers.com/index.html

Useful links


Conferences and meetings

See Conferences

Scientific challenges and competitions

CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/

Assemblathon

Variathon: http://bioinf.dimi.uniud.it/variathon

Alignathon

Sequence squeeze: http://www.sequencesqueeze.org/

Resources for researchers

http://www.protocol-online.org/science-forums-2/Dissertation-and-Paper-Writing/

http://www.protocol-online.org/science-forums-2/Career-Advice/

https://www.researchgate.net

http://friendfeed.com/the-life-scientists

http://nigerianbioscientist.com/

Educational resources

http://www.bioinformatics.nl/molbi/SimpleCloningLab/index.htm

ROSALIND Bioinformatics challenges: http://rosalind.info/problems/locations/

Project Euler: http://projecteuler.net/

AddGene molecular biology reference: http://www.addgene.org/mol_bio_reference/

https://www.manylabs.org/

http://www.dnalabbook.co.uk/

Wiki sites

http://www.scholarpedia.org

SNPedia.com

http://www.wikigenes.org

http://ecoliwiki.net

http://www.phylocommons.org/

Discussion and communities

Apps

mPartsregistry: http://mpartsregistry.appspot.com

Persons/Research groups

http://genefish.wikispaces.com/

Mark Pallen: http://www2.warwick.ac.uk/fac/med/research/microinfect/staff/pallengroup/

Chris Anderson lab: https://andersonlab.qb3.berkeley.edu/

Magni Paolo: http://www.labmedinfo.org/people/magni

http://www.rpgroup.caltech.edu/publications/

Heng Li. "Alignment God".

Dworkin lab: https://www.msu.edu/~idworkin/publications.html

Titus Brown:

Erlich lab: http://erlichlab.wi.mit.edu/index.html

Cristopher mason: http://www.masonlab.net/

http://openwetware.org/wiki/User:Vincent

Markus Gershater

http://www.princeton.edu/~ajlgroup/

Heng Li

Michael Cashel: https://science.nichd.nih.gov/confluence/display/pgd/Michael+Cashel+Lab

Jim Collins: http://www.bu.edu/abl/

Jason Kelly: http://openwetware.org/wiki/Jason_Kelly

Tom Ellis: http://openwetware.org/wiki/User:Ellis

George Church: http://arep.med.harvard.edu/gmc/

Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html

Chris Voigt

Bernahrd Ø Pallsson: http://gcrg.ucsd.edu/Researchers/Palsson

Tom Knight

Joe Felsenstein: http://www.gs.washington.edu/faculty/felsenstein.htm

  • Professor of Genome Sciences and Biology, University of Washington.

Drew Endy: http://openwetware.org/wiki/User:Endy

Densmore lab: http://people.bu.edu/dougd/research.html

Ron Weiss: http://groups.csail.mit.edu/synbio/people/professor-ron-weiss/

Jean Peccoud

Jonathan Eisen

Martin Fusenegger

Pamela Silver

Rob Carlson

Ethan Perlstein: http://www.perlsteinlab.com/

Anthony Evans

Nick Loman:

http://pathogenomics.bham.ac.uk/clinicogenomics/

http://pathogenomics.bham.ac.uk/blog/author/nick/

Titus Brown: http://ivory.idyll.org/blog/category/science.html

Lex Nedebragt:

http://contig.wordpress.com/

https://twitter.com/lexnederbragt

Manual Corpas:

Barry L Wanner: https://www.bio.purdue.edu/molecular_biosciences/directory.php?refID=30

  • Made many E. coli strains.

Andrew Hessel: http://andrewhessel.com/

Societies and associations

Society for applied microbiology: http://www.sfam.org.uk/

American Association for Clinical Chemistry : http://www.aacc.org/Pages/default.aspx

Royal Society of Chemistry: http://www.rsc.org/

Society for general microbiology: http://www.sgm.ac.uk/

American society for microbiology: http://www.asm.org/

Norsk Kjemisk selskap: http://www.kjemi.no/

International Society for Systems Biology: http://www.issb.org/

Genetics Society of America: http://www.genetics-gsa.org/

British Society for Gene and Cell Therapy: https://www.facebook.com/BSGCT

American Society of Human Genetics (ASHG):

Society for Molecular Biology and Evolution (SMBE): http://www.smbe.org/

Publications

Journal name Publisher Open access status Link
ACS Synthetic Biology American Chemical Society No http://pubs.acs.org/journal/asbcd6
Bioengineered (Previously: Bioengineered bugs) Landes Bioscience Partial http://dev.landesbioscience.com/journals/bioe/
Bioinformatics Oxford Journals http://bioinformatics.oxfordjournals.org/
Biology Open Company of Biologists Yes http://bio.biologists.org/
BMC Medical Genomics BMC Yes http://www.biomedcentral.com/bmcmedgenomics/
BMC Proceedings BMC Yes http://www.biomedcentral.com/bmcproc
PLOS One Public Library of Science Yes http://www.plosone.org/
Nucleic Acids Research Oxford Journals Yes http://nar.oxfordjournals.org/
BMC Systems Biology BioMedCentral Yes http://www.biomedcentral.com/bmcsystbiol/
BMC Microbiology BioMedCentral Yes http://www.biomedcentral.com/bmcmicrobiol
Cell Cell Press http://www.cell.com/
Cell Reports Cell Press Yes http://cellreports.cell.com/
The EMBO Journal Nature Publishing Group No http://www.nature.com/emboj/index.html
Frontiers in Synthetic Biology Nature Publishing Group http://www.frontiersin.org/Synthetic_Biology/about
Genetics Genetics Society of America http://www.genetics.org/
G3: Genes, Genomes, Genetics Mission Genetics Society of America http://www.g3journal.org/
Genome Research Cold Spring Harbor Press Partial (6 month embargo) http://genome.cshlp.org/
Genome Biology BMC Yes http://genomebiology.com/
Genome Medicine BioMedCentral Yes http://genomemedicine.com/
Journal of Experimental Biology Company of Biologists http://jeb.biologists.org/
Journal of molecular biology Elsevier Partial http://www.journals.elsevier.com/journal-of-molecular-biology/
Journal of biological chemistry American Society for Biochemistry and Molecular Biology. No http://www.jbc.org/
Journal of bacteriology American Society for Microbiology No http://jb.asm.org/
Journal of Bioscience and Engineering http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
Journal of clinical microbiology American Society for Microbiology No http://jcm.asm.org/
mBio ASM Yes http://mbio.asm.org/
Methods Elsevier No http://www.journals.elsevier.com/methods
Microbiology SGM/HighWire Press No http://mic.sgmjournals.org/
Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology Reviews ASM mmbr.asm.org
Metabolic Engineering Elsevier Partial http://www.journals.elsevier.com/metabolic-engineering/
Molecular Systems Biology EMBO/Nature Publishing Group Yes http://www.nature.com/msb/index.html
PLOS Computational Biology Public Library of Science Yes http://www.ploscompbiol.org/
PLOS Pathogens PLOS Yes http://www.plospathogens.org/
Proceedings of the National Academy of Sciences National Academy of Sciences No http://www.pnas.org/
Protein expression and purification Elsevier No http://www.sciencedirect.com/science/journal/10465928
Genome Announcements ASM Yes http://genomea.asm.org/
Futures Elsevier ? http://www.sciencedirect.com/science/journal/00163287
Microbial Cell Factories BioMedCentral Yes http://www.microbialcellfactories.com/
Engineering Studies Taylor & Francis  ? http://www.tandfonline.com/loi/test20
FEMS Microbiology Reviews http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
Nature Biotechnology Nature Publishing Group No http://www.nature.com/nbt/index.html
Nature Genetics Nature Publishing group No http://www.nature.com/ng/index.html
Plasmid Elsevier No http://www.journals.elsevier.com/plasmid/
Journal of Computational Biology Liebert Publishing No http://www.liebertpub.com/CMB
Trends in Biochemical Sciences Elsevier http://www.sciencedirect.com/science/journal/09680004
Trends in Microbiology Elsevier/Cell Press http://www.sciencedirect.com/science/journal/0966842X
Molecular Genetics & Genomic Medicine Wiley Yes http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
Molecular genetics and genomics Springer Verlag http://link.springer.com/journal/438
Biochemistry and Molecular Biology Education Wiley No http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
Current opinion in chemical biology Elsevier http://www.sciencedirect.com/science/journal/13675931
New England Journal of Medicine NEJM Group http://www.nejm.org/
Systems and Synthetic Biology Springer http://link.springer.com/journal/11693
Scientific Reports Nature Publishing Group Yes http://www.nature.com/srep/index.html


Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/

Computational and Structural Biotechnology Journal


http://www.journalnetwork.org/journals/science-general/citizen-science/citizen-science-innovation.html

Biotechniques: http://www.biotechniques.com/

https://www.openlibhums.org/

Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727

http://www.g3journal.org/

http://push.cwcon.org/

eLife: http://elife.elifesciences.org/

https://peerj.com/

Faculty of 1000: http://f1000.com/


Social Science Research Network: http://www.ssrn.com/


Open access:

http://en.wikipedia.org/wiki/List_of_open-access_journals

http://scholarlyoa.com/

http://www.doaj.org/

http://www.opendoar.org/

http://blogs.scientificamerican.com/guest-blog/2013/04/03/who-killed-the-preprint-and-could-it-make-a-return/

Publication tools:

https://collage.elsevier.com/

Reference management / Social bookmarking:

http://www.mendeley.com/

http://www.citeulike.org/

JabRef reference manager: http://jabref.sourceforge.net/

Publishers

Springer

Elsevier

CRC Press

Horizon Press

Databases/Repositories

PlasmID database: http://plasmid.med.harvard.edu/PLASMID/

Addgene plasmid repository: http://www.addgene.org/

DNASU plasid repository: http://dnasu.asu.edu/DNASU/

The Open Construct Database: http://www.the-odin.com

Bionumbers - The database of useful biological numbers

EcoCyc - E. coli K-12 MG1655 database: http://www.ecocyc.org/

EcoGene: http://www.ecogene.org

JWS Online model database: http://jjj.biochem.sun.ac.za/database/

http://systems-biology.org/resources/model-repositories/

Genome-Scale metabolic network database: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm

Array express: http://www.ebi.ac.uk/arrayexpress/

Rebase restriction enzyme database: http://rebase.neb.com/rebase/rebase.html

1000 genomes project: http://browser.1000genomes.org/index.html

BRENDA Enzymes: http://www.brenda-enzymes.info/

KEGG

GenBank

http://datadryad.org/

http://www.cathdb.info/

Codon usage

http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333

Codon usage analyzer: http://www.bioinformatics.org/sms2/codon_usage.html

Other informational resources

National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html

http://seqanswers.com

NCBI vs EMBL vs DDBJ.: http://lib.bioinfo.pl/courses/view/151

The DDBJ/EMBL/GenBank Feature Table Definition: http://www.insdc.org/files/feature_table.html#1

http://openwetware.org/wiki/DNA - Contains many protocols

Bite Size Bio: http://bitesizebio.com/

BenchFly: http://www.benchfly.com/

http://biologicalworld.com/protocols.htm

http://www.methods.info/

http://www.biotechdaily.com/

http://www.zenbiology.com/

http://www.my-whiteboard.com/

http://lablife.org

http://www.molbiol-tools.ca/

http://www.molecularinfo.com/MTM/MTM.html

http://www.openhelix.com/ - Genomics and bioinformatics resources.

Programming

BioPython: http://biopython.org/wiki/Main_Page

CodEval - programming challenges: http://codeeval.com/

Law and ethics

http://www.genomicslawreport.com/

American journal of Bioethics: http://www.tandfonline.com/toc/uajb20/current

IASB Code of Conduct for best practices in gene synthesis: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/code-of-conduct-for-best-practices-in-gene-synthesis/

IASB - About Biosafety & Security: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/biosafety-biosecurity/

Andrew W Torrance on DNA copyright: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2017670


Cloning

SLIC, Gibson, CPEC and SLiCE assembly methods: http://j5.jbei.org/j5manual/pages/22.html

RF cloning: http://www.rf-cloning.org/QandA.php

PCR Primer design: http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm

PCR: http://www.molbiol-tools.ca/PCR.htm

OpenWetWare - designing primers: http://openwetware.org/wiki/Designing_primers

PCR Guide: http://medicine.yale.edu/labs/henegariu/www/tavi/Guide.html

PCR troubleshooting: http://medicine.yale.edu/labs/henegariu/www/tavi/Trblesht.html

DNA Tm estimation methods: http://openwetware.org/wiki/Primer_Tm_estimation_methods

DNA stability: http://openwetware.org/wiki/DNA_stability

E. coli cloning checklist: http://openwetware.org/wiki/Cloning_Checklist

Guide to Gibson assembly: http://www.synbio.org.uk/dna-assembly/guidetogibsonassembly.html

Primer design guidelines: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html

Sequencing

Design of sequencing primers: http://seqcore.brcf.med.umich.edu/doc/dnaseq/primers.html

Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi: http://biology.duke.edu/fungi/mycolab/primers.htm

GenScript DNA Sequencing Primers Design Tool: http://www.genscript.com/cgi-bin/tools/sequencing_primer_design

Software tools

Molecular Biology Freeware for Windows: http://molbiol-tools.ca/molecular_biology_freeware.htm#Graphic%20packages

Molecular Biology & Bioinformatics Resources: http://library.weill.cornell.edu/eresources/molbio.html

Bioinformatics Tools and Resources for Biomedical Scientists and Students - http://www.changbioscience.com/virtualab.html


DNA copy number calculator: http://www.uri.edu/research/gsc/resources/cndna.html

Graphics software:

Systems Biology

http://systems-biology.org/

Cytoscape: www.cytoscape.org

CAIN stochastic simulations for chemical kinetics: http://cain.sourceforge.net/

COBRA Constraints-based modelling toolbox:

CellNetAnalyzer: http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html

CellDesigner: http://celldesigner.org/

OptFlux: http://www.optflux.org/

Systems Biology Markup Language: www.sbml.org

SBML to LaTex report generator: http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/index.html

Systems Biology Toolbox 2 for MATLAB: http://www.sbtoolbox2.org/main.php

http://www.sysbio.de/

Handbook of Systems Biology: http://www.sciencedirect.com/science/book/9780123859440

Reflexive Systems Biology: http://portal.cbu.uib.no/rsb

Bioinformatics & Annotation

Neural Network Promoter Prediction: http://www.fruitfly.org/seq_tools/promoter.html

Artemis genome browser: http://www.sanger.ac.uk/resources/software/artemis/

BASYS Bacterial Annotation software: http://basys.ca/

SoftBerry: http://linux1.softberry.com/berry.phtml

Promethease: http://snpedia.com/index.php/Promethease

GLIMMER microbial gene-finding system: http://www.cbcb.umd.edu/software/glimmer/

Promoter & termination site search tools: http://molbiol-tools.ca/Promoters.htm

Phyre 2 - protein fold recognition: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

FITBAR DNA binding protein binding site predictor: http://archaea.u-psud.fr/fitbar/

Simple Consensus Maker: http://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html

Model SEED - blog: http://blog.theseed.org/model_seed/

Model SEED - Viewer: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView

http://www.bioinformatics.org/

Plasmid map drawer: http://www.rf-cloning.org/savvy.php

EMBOSS ((European Molecular Biology Open Software Suite): http://bips.u-strasbg.fr/EMBOSS/

BioBrick -> GenBank converter: http://2010.igem.org/Team:Cambridge/Tools/GenBank


HMMER: http://hmmer.janelia.org/

Jcat Codon Adaption Tool: http://www.jcat.de/

Cloning & Construction

The Constructor: http://2011.igem.org/Team:Wageningen_UR/Softwaretool/

NEBcutter: http://tools.neb.com/NEBcutter2/

J5 automated DNA assembly: http://j5.jbei.org/index.php/Main_Page

Genome Compiler: http://www.genomecompiler.com/

Gibthon: http://django.gibthon.org/


Transcription and Translation: http://www.attotron.com/cybertory/analysis/trans.htm

All-IN-ONE SEQ-ANALYZER: http://www-personal.umich.edu/~ino/blast.html


GENtle 2: http://ec2-23-20-169-157.compute-1.amazonaws.com/dev/#

DNA oligomer design tools:

Primer-BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/

QuickChange primer design script: http://sosnick.uchicago.edu/stuff/quickchanger.pl

IDT SciTools - oligo design and analysis: http://eu.idtdna.com/scitools/scitools.aspx

PrimerDigital: http://primerdigital.com/tools/

Primer3: http://primer3.wi.mit.edu/

Primer3 plus: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

InvitroGen OligoPerfect designer: http://tools.invitrogen.com/content.cfm?pageid=9716

PrimerQuest: www.idtdna.com/Scitools/Applications/Primerquest/

JCVI Primer designer: http://primerdesigner.sourceforge.net/

Primer Design Assistant: http://dbb.nhri.org.tw/primer/index.html

PrimerZ: http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

Primo PCR Primer Design: http://www.changbioscience.com/primo/primo.html

Eurofins PCR primer design: https://ecom.mwgdna.com/services/webgist/pcr_primer_design_new.tcl?ot=OLIGO_PCRD&item_id=new

Eurofins Sequencing primer design: https://ecom.mwgdna.com/services/manage-primers/design-primer.tcl

DNA/oligomer property calculators:

http://www.basic.northwestern.edu/biotools/oligocalc.html

In silico PCR tools:

http://exon.ucsc.edu/cgi-bin/hgPcr

http://insilico.ehu.es/PCR/

http://www.bioinformatics.org/sms2/pcr_products.html

http://qsnp.gen.kyushu-u.ac.jp/genome/InSilicoPCR.html

http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold

http://www.molbiol-tools.ca/Repeats_secondary_structure_Tm.htm

Protocols

http://www.protocolpedia.com/

OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols

Springer Protocols: http://www.springerprotocols.com

Complementary annealing of oligonucleotides: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html

Knight lab - annealing protocol: http://openwetware.org/wiki/Knight:Annealing_and_primer_extension_with_Taq_polymerase

Knight lab -restriction digest protocol: http://openwetware.org/wiki/Knight:Restriction_Digest

Endy: Colony PCR: http://openwetware.org/wiki/Endy:Colony_PCR

Addgene Moleular cloning guide: http://www.addgene.org/plasmid_reference/index/#cloning

Addgene restriction digest protocol: http://www.addgene.org/plasmid_protocols/restriction_digest/

http://www.addgene.org/plasmid_protocols/bacterial_plates/

http://www.methods.info/Methods/RNA_DNA/restr_analysis.html

http://www.methodbook.net/dna/restrdig.html

Current Protocols: http://www.currentprotocols.com

Science Advisory Board - protocols: http://www.scienceboard.net/resources/protocols.asp?criteria=

Protocol online: http://protocol-online.org/

http://site.methodological.co/

http://bio-protocol.org/

Misc.

http://www.nature.com/scitable

https://www.assaydepot.com/

https://www.scienceexchange.com/

http://matt.might.net

http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html

http://www.phdontrack.net/

Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm

J Craig Venter Institute - software: http://www.jcvi.org/cms/research/software/

DNA sequence transformation tools: http://molbiol-tools.ca/Convert.htm

The Oligator: http://gcat.davidson.edu/igem10/tutorial.html

http://www.zappylab.com/apps

Nucleic Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm

String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn

ProtLifePred protein lifetime calculator: http://protein-n-end-rule.leadhoster.com/

See also: http://2012.igem.org/User_talk:Jarlemag and http://2012.igem.org/Team:NTNU_Trondheim/Links

US National Human Genome Research Institute: http://www.genome.gov/

Codon table: http://en.wikipedia.org/wiki/DNA_codon_table

LaTeX lab book: http://openwetware.org/wiki/LabbookInLatex

Los Alamos Technical Reports collection: http://www.sciencemadness.org/lanldocs.html

http://thelabrat.com

The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home

NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/

http://www.lablit.com/


Addgene - Genome engineering Guide: https://www.addgene.org/Genome_Engineering/?utm_source=Addgene+March+14%2C+2013+Newsletter+Final&utm_campaign=March+2013+Newsletter&utm_medium=email

https://genomeinterpretation.org

Science News & Discussion

Magazines/Blogs/Newssites

http://www.labcritics.com/

http://scienceblok.com/

http://sciblogs.co.nz/

http://www.scicentral.com/index.html

http://blogs.discovermagazine.com/seriouslyscience/

http://epigenie.com/

http://www.livescience.com/

http://scienceblogs.com/

http://scientopia.org/blogs/

The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#

SciTech Daily: http://scitechdaily.com/

The Scientist: http://www.the-scientist.com/

GEN Magazine: http://www.genengnews.com/

Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467

http://www.reportergene.com/

Super awesome Sylvia: http://sylviashow.com/

http://www.technologyreview.com/

http://www.scilogs.com/

Blogs:

http://ironchefsynbio.wordpress.com/

http://retractionwatch.wordpress.com/

http://www.genomesunzipped.org/

http://ing.dk/blogs/folkeforsker

http://phylogenomics.blogspot.no/

http://88proof.com/synthetic_biology/blog/

http://bytesizebio.net

The hardest science - a psychology blog: http://hardsci.wordpress.com/

http://dienekes.blogspot.no/

Michael Eisen - It's Not Junk: http://www.michaeleisen.org/blog/

Open Helix: http://blog.openhelix.eu/

http://ivory.idyll.org/

http://titojankowski.com/

See also http://www.microbe.net/microbiology-blogs/

Aggregators:

http://paper.li/SAGRudd/1323661247

http://paper.li/leclercfl/bioscience

The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246 Norwegian:

http://thaliana.blogg.no/1290598240_molekylrbiologi.html

Social & personalized media:

http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat

http://trap.it/


Discussion sites:

http://pubpeer.com/

In the news/Commentaries

George Church - Reading and writing omes: http://www.nature.com/msb/journal/v9/n1/full/msb201275.html

Synthetic Biology comes down to Earth: http://chronicle.com/article/Synthetic-Biology-Comes-Down/137587/

Predictability - the brass ring for synthetic biology: http://newscenter.lbl.gov/science-shorts/2013/03/13/predictability-the-brass-ring-for-synthetic-biology/

Press Release - Bootstrapping Biotechnology: Engineers Cooperate to Realize Precision Grammar for Programming Cells http://www.synberc.org/bootstrapping-biotechnology

HeLa genome sequenced: http://www.embl-hamburg.de/aboutus/communication_outreach/media_relations/2013/130311_Heidelberg/index.html

Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html


Badomics: http://www.gigasciencejournal.com/content/1/1/6

http://keithbradnam.com/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html

Jobs

https://www.odesk.com/

http://www.tu.no/jobb/

http://www.aftenposten.no/jobb/

http://www.ingeniorstillinger.no/

http://no.indeed.com/jobs?q=Ingeni%C3%B8r&gclid=CJL3_IiL47YCFQdd3godpBMArQ

http://www.nature.com/naturejobs/science/jobs

http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152

http://yes.jucan.no/

https://uio.easycruit.com/


Tips:

Search professional/business search sites for companies in fields of interest. Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.

Games

BioHack: http://marketplace.xbox.com/en-US/Product/BioHack/66acd000-77fe-1000-9115-d802585505ee

http://eterna.cmu.edu/web/

http://adamilab.msu.edu/evolve-and-conquer/

http://fold.it/portal/

http://phylo.cs.mcgill.ca/ (publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031362)

http://io9.com/these-cool-games-let-you-do-real-life-science-486173006

http://www.citizensort.org/

http://sourceforge.net/projects/brainworkshop/?source=directory

Just for Fun

Origin of the Species in Dub: http://pathogenomics.bham.ac.uk/Dub/origin.html

NCBI ROFL: http://blogs.discovermagazine.com/discoblog/category/ncbi-rofl/

The PCR song: http://www.youtube.com/watch?v=x5yPkxCLads

Biorad GTCA song: http://www.youtube.com/watch?NR=1&feature=endscreen&v=ID6KY1QBR5s

iGEM style! http://www.youtube.com/watch?v=KHhswxo6xow

English Tea Time Gene: http://partsregistry.org/Part:BBa_J49005

Trust me, I'm an engineer: http://www.youtube.com/watch?v=rp8hvyjZWHs

I'm an Engineering failure: http://www.youtube.com/watch?v=ro3EPPYbn44

DNA text codec: http://www.sgidna.com/translator.php

Funny bioinformatic tool names: http://www.biostars.org/p/67874/

http://abstrusegoose.com

http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/

Enclothed cognition: http://www.sciencedirect.com/science/article/pii/S0022103112000200

robotniknin: http://www.ncbi.nlm.nih.gov/pubmed/19151731 .


Arxiv vs Snarxiv: http://snarxiv.org/vs-arxiv/

YouTube

https://groups.google.com/forum/?fromgroups=#!topic/diybio/yXfghy7a7wc


http://www.youtube.com/watch?v=mOgTVx9ge5M&feature=player_embedded


http://www.youtube.com/user/basementbiotech

http://www.youtube.com/watch?v=odxvp-3nSw4

Success in Science in 16 minutes: http://www.youtube.com/watch?v=r0vBS0oC8aM

Favorites

Favorite things of all kinds:

Bioinformatics blogs:

http://www.homolog.us/blogs/

To read

Composability of regulatory sequences controlling transcription and translation in E. coli.