User:Jarle Pahr
Contact Info
- Jarle Pahr
- Norwegian University of Science and Technology
jarlemag@stud.ntnu.no
Education
2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology
Research interests
- Omega-3/poly-unsaturated fatty acid biosynthesis
- Metabolic networks & Metabolic engineering
- Molecular genetics of lactate utilization in bacteria
- Bacterial stringent response
Notes
Projects
Organisms
Escherichia coli
Mesoplasma florum
http://openwetware.org/wiki/Mesoplasma_florum
http://partsregistry.org/Mesoplasma_florum
http://microbewiki.kenyon.edu/index.php/Mesoplasma_florum
http://www.broadinstitute.org/annotation/genome/mesoplasma_florum
M. florum genome-scale model: http://biomodels.caltech.edu/BMID000000141045
Rhodococcus opacus
http://www.broadinstitute.org/blog/creature-feature-rhodococcus-opacus-pd630 http://mic.sgmjournals.org/content/146/5/1143.full.pdf
B. subtilis
C. glutamicum
Lactobacillus bulgaricus
http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus
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
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/
Research programs/projects
Statseq: http://www2.ab.wur.nl/statseq/
Online learning
Portals:
MIT Open Courseware: http://ocw.mit.edu/index.htm
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
Language
Chinese
http://english.cntv.cn/learnchinese/
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://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:
Speaking:
SpeakGoodChinese: http://www.speakgoodchinese.org/
Synthetic Biology
www.synthetic-bestiary.com
Competitions and challenges:
http://www.ia-sb.eu/go/synthetic-biology/
LabGenius: www.labgeni.us
Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/
Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html
TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering: http://synthetic-biology.bbn.com/tasbe.html
Raytheon BBN Synthetic biology publications: http://synthetic-biology.bbn.com/pubs.html'
BBN Synthetic biology tools: https://synbiotools.bbn.com/
Biological part collections
https://biobricks.org/bpa/find-a-part/
DYI Bio/Citizen science
http://www.brightworkcoresearch.com/
http://portlabpdx.org/wiki/index.php?title=Main_Page
http://www.pietervanboheemen.nl/
http://citizensciencequarterly.com/
http://www.citizensciencecenter.com/?gclid=CJLtwKXoprcCFczC3god6U4Ahw
http://diyhpl.us/wiki/diybio/faq/
http://blogs.plos.org/citizensci/
DYI Bio Europe: http://www.diybio.eu/
Open PCR: http://openpcr.org/
www.indiebiotech.com
Ask a Biosafety expert: http://ask.diybio.org/
Public Laboratory: http://publiclaboratory.org/home
BOSSLAB: http://bosslab.org/
Science hideout: http://www.youtube.com/user/ScienceHideout
BiologiGaragen: http://biologigaragen.org/
http://haberlandt.blablablab.org/
Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs
Bibliography:
Process, Not Product: Investigating Recommendations for Improving Citizen Science “Success” : http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064079
Crowdfunding
Projects:
http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit
http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
Contract research services
https://www.scienceexchange.com/
Home experiments/projects
(Legality may vary depending on your location)
How to do a pGlo transformation: http://www.youtube.com/watch?v=sovDqqhQJx8
http://www.instructables.com/id/The-Light-Fountain-a-Bioluminescent-Hourglass/
http://cibt.bio.cornell.edu/workshops_and_summer_programs/0608alum/lumos.pdf
http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/%3Eprotocol
Art and Strategy
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/
Personal genomics
http://www.genomesunzipped.org/
uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
http://www.personalgenomes.org/
Companies
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/
Cambrian Genomics: https://angel.co/cambrian-genomics http://cambriangenomics.com/
Suppliers
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/
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/
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://www.sbsbio.com/english/dnahc.html
http://www.interfarm.no/produkter/
Used equipment vendors:
http://www.labrecyclers.com/index.html
Useful links
Conferences and meetings
Synthetic Biology:
SBx.0: http://sb6.biobricks.org/
Applications for Synthetic Biology in Industrial Biotechnology 2013: http://www.clocate.com/conference/Applications-for-Synthetic-Biology-in-Industrial-Biotechnology-2013/38757/
Genomics:
Advances in Genome Biology and Technology: http://agbt.org/about.html
European Human Genetics Conference
Personal Genomes & Medical Genomics (PGMG) (Cold Spring Harbor Laboratories meeting).
Biology of Genomes (BOG): https://meetings.cshl.edu/meetings/2013/genome13.shtml
Beyond the Genome: http://www.beyond-the-genome.com/
Understand Your Genome (UYG): http://www.illumina.com/company/events/understand-your-genome.ilmn
American Society of Human Genetics (ASHG) annual meeting: http://www.ashg.org/2013meeting/
Other:
International Conference on Computational Cell Biology: http://www.cpe.vt.edu/ccb/index.html
General Meeting, American Association for Microbiology (ASM): http://gm.asm.org/
Balti and bioinformatics: http://pathogenomics.bham.ac.uk/blog/2013/04/balti-and-bioinformatics-midlands-sequencing-and-bioinformatics-meeting-monday-20th-may-2013/
Bioinformatics Open Source Conference (BOSC): http://www.open-bio.org/wiki/BOSC_2013
Galaxy Community Conference: http://wiki.galaxyproject.org/Events/GCC2013
Scientific challenges and competitions
CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/
Assemblathon
Variathon: http://bioinf.dimi.uniud.it/variathon
Alignathon
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/
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/
Wiki sites
SNPedia.com
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/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
Apps
mPartsregistry: http://mpartsregistry.appspot.com
Persons/Research groups
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
Pallsson
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/blog/author/nick/
Titus Brown: http://ivory.idyll.org/blog/category/science.html
Lex Nedebragt:
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/
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/ | ||
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 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 Medicine | BioMedCentral | Yes | http://genomemedicine.com/ | |
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 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/ | |
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 | |
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 | ||
Molecular Genetics & Genomic Medicine | Wiley | Yes | http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269 | |
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 |
Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/
Biotechniques: http://www.biotechniques.com/
Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727
eLife: http://elife.elifesciences.org/
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
Publication tools:
Reference management / Social bookmarking:
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
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
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.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
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
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://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
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/
Misc.
http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html
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
Nuclei 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
The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home
NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/
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
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/
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
Super awesome Sylvia: http://sylviashow.com/
http://www.technologyreview.com/
Blogs:
http://retractionwatch.wordpress.com/
http://www.genomesunzipped.org/
http://ing.dk/blogs/folkeforsker
http://phylogenomics.blogspot.no/
http://88proof.com/synthetic_biology/blog/
The hardest science - a psychology blog: http://hardsci.wordpress.com/
Michael Eisen - It's Not Junk: http://www.michaeleisen.org/blog/
Open Helix: http://blog.openhelix.eu/
See also http://www.microbe.net/microbiology-blogs/
Norwegian:
http://thaliana.blogg.no/1290598240_molekylrbiologi.html
Social & personalized media:
http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
Discussion sites:
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
Jobs
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
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
http://adamilab.msu.edu/evolve-and-conquer/
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
Just for Fun
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://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 .
YouTube
https://groups.google.com/forum/?fromgroups=#!topic/diybio/yXfghy7a7wc
Favorites
Favorite things of all kinds:
Bioinformatics blogs: