User:Jarle Pahr

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Revision as of 09:28, 23 June 2013

Contents

Contact Info

Jarle Pahr
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

Algorithms

Articles

Automation

Apps

16S RNA

Beer

Biology

Biofilms

Biofuel

Bitesize Biology

BioBricks

Bioprospecting

Bioinformatics

BAMBI

BAMBI-LAST

BAMBI-FAST

BLAST

Blogs

Books

Buffers

Cancer

Chemistry

Calculations

Centrifugation

Characterising

Checklists

Chemicals

Competent cells

Cloning

Cloud computing

Computation

Colicins

Control theory

Data analysis

Databases

Degradation tags

DNA

Electrophoresis

Electronics

Epigenetics

Ethics

Experiments

Experimental design

Expression

Equipment

Evolution

Food

Flux Balance Analysis

Genes

Genetic circuits

Gene therapy

Genetic engineering

Genomes

GMO

GFP

Genetics

Kits

Graph theory

Growth media

Hardware

Health

History of science

iGEM

Invisibility

Laboratory software

LaTeX

Networks

Lab lessons

Lac operon

Lux operon

Ligation

Liquid handling

Biological computation

Medicine

Mutations

Microscopy

Models

Microbiology

Noise

Organisms

Optogenetics

Oligonucleotides

Pathogens

pH

Simulations

Open science

Patents

Persistence

Plasmids

Phylogenetics

Promoters

Protocols

PCR

Programming

RelA

Refuted

Robotics

Research questions

Recipes

Restriction

RNA

Safety

Storage

Single cell technologies

Software

Stringent response

Statistics

Strains

Sterilization

Synthetic Biology

Systems Biology

Transformation

Theses

Vectors

Verification

Writing lessons

Yeast

Yoghurt

Wine

Projects

ppGpp MSc. project

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

http://bsubcyc.org/

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/

http://korflab.ucdavis.edu/

Research programs/projects

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

Online learning

http://www.skillshare.com/

Portals:

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

http://www.core.org.cn

https://www.coursera.org/

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

https://www.udacity.com/

https://www.edx.org/courses

https://www.khanacademy.org

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://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

www.synthetic-bestiary.com

http://www.synbioproject.org/

http://www.synbiont.org/

Competitions and challenges:

http://igem.org

http://genocon.org/

http://www.ia-sb.eu/go/synthetic-biology/

LabGenius: www.labgeni.us

http://synbio.org.uk/

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/

http://www.synberc.org/

http://www.teselagen.com/

Biological part collections

http://partsregistry.org

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

https://registry.synberc.org/

DYI Bio/Citizen science

http://hivebio.org/

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://bamh1.com/

http://diyhpl.us/wiki/diybio/faq/

http://www.lapaillasse.org

http://openbioprojects.net/

http://hackteria.org/

http://blogs.plos.org/citizensci/

http://diybioftw.com/

http://dyibio.org

DYI Bio Europe: http://www.diybio.eu/

http://genefoo.com/

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/

http://biocurious.org/

http://genspace.org/

Science hideout: http://www.youtube.com/user/ScienceHideout

http://basementbiotech.org/

http://www.biotinker.com/

BiologiGaragen: http://biologigaragen.org/

http://haberlandt.blablablab.org/

http://www.bugssonline.org/

Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs

http://roningenetics.org/

https://www.biotinkering.org/


Bibliography:

Process, Not Product: Investigating Recommendations for Improving Citizen Science “Success” : http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064079


Crowdfunding

https://www.gittip.com/about/

http://scifundchallenge.org/

http://www.kickstarter.com/

https://www.microryza.com/

http://www.indiegogo.com/

http://www.gofundme.com/

http://www.rockethub.com/

http://www.scistarter.com/

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/

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

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

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://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

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/


International Workshop on Biologigal design automation: http://iwbda2012.csb.pitt.edu/mediawiki/index.php/Main_Page

Genomics:

Advances in Genome Biology and Technology (AGBT): 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

http://pathogenomics.bham.ac.uk/blog/2013/03/applied-bioinformatics-public-health-microbiology-15-17-may-2013/

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

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

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

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

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:

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/
BioinformaticsOxford Journals http://bioinformatics.oxfordjournals.org/
Biology OpenCompany of BiologistsYeshttp://bio.biologists.org/
BMC Medical GenomicsBMCYeshttp://www.biomedcentral.com/bmcmedgenomics/
BMC ProceedingsBMCYeshttp://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 BiologyBioMedCentralYeshttp://www.biomedcentral.com/bmcsystbiol/
BMC MicrobiologyBioMedCentralYeshttp://www.biomedcentral.com/bmcmicrobiol
CellCell Press http://www.cell.com/
Cell ReportsCell Press Yeshttp://cellreports.cell.com/
The EMBO JournalNature Publishing Group Nohttp://www.nature.com/emboj/index.html
Frontiers in Synthetic BiologyNature Publishing Group http://www.frontiersin.org/Synthetic_Biology/about
GeneticsGenetics Society of America http://www.genetics.org/
G3: Genes, Genomes, Genetics Mission Genetics Society of America http://www.g3journal.org/
Genome ResearchCold Spring Harbor PressPartial (6 month embargo) http://genome.cshlp.org/
Genome BiologyBMCYeshttp://genomebiology.com/
Genome MedicineBioMedCentralYeshttp://genomemedicine.com/
Journal of Experimental BiologyCompany of Biologistshttp://jeb.biologists.org/
Journal of molecular biologyElsevier Partialhttp://www.journals.elsevier.com/journal-of-molecular-biology/
Journal of biological chemistryAmerican Society for Biochemistry and Molecular Biology. Nohttp://www.jbc.org/
Journal of bacteriologyAmerican Society for Microbiology Nohttp://jb.asm.org/
Journal of Bioscience and Engineering http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
Journal of clinical microbiologyAmerican Society for MicrobiologyNohttp://jcm.asm.org/
mBioASMYeshttp://mbio.asm.org/
MethodsElsevierNohttp://www.journals.elsevier.com/methods
MicrobiologySGM/HighWire PressNohttp://mic.sgmjournals.org/
Metabolic EngineeringElsevierPartialhttp://www.journals.elsevier.com/metabolic-engineering/
Molecular Systems BiologyEMBO/Nature Publishing GroupYeshttp://www.nature.com/msb/index.html
PLOS Computational BiologyPublic Library of ScienceYeshttp://www.ploscompbiol.org/
PLOS PathogensPLOSYeshttp://www.plospathogens.org/
Proceedings of the National Academy of SciencesNational Academy of SciencesNohttp://www.pnas.org/
Protein expression and purificationElsevierNohttp://www.sciencedirect.com/science/journal/10465928
Genome AnnouncementsASMYeshttp://genomea.asm.org/
FuturesElsevier?http://www.sciencedirect.com/science/journal/00163287
Microbial Cell FactoriesBioMedCentralYeshttp://www.microbialcellfactories.com/
Engineering StudiesTaylor & Francis ?http://www.tandfonline.com/loi/test20
FEMS Microbiology Reviews http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
Nature BiotechnologyNature Publishing GroupNohttp://www.nature.com/nbt/index.html
Nature GeneticsNature Publishing groupNohttp://www.nature.com/ng/index.html
PlasmidElsevierNohttp://www.journals.elsevier.com/plasmid/
Journal of Computational BiologyLiebert PublishingNohttp://www.liebertpub.com/CMB
Trends in Biochemical SciencesElsevier http://www.sciencedirect.com/science/journal/09680004
Molecular Genetics & Genomic MedicineWileyYeshttp://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
Biochemistry and Molecular Biology EducationWileyNohttp://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
Current opinion in chemical biologyElsevier http://www.sciencedirect.com/science/journal/13675931
New England Journal of MedicineNEJM Group http://www.nejm.org/
Systems and Synthetic BiologySpringer http://link.springer.com/journal/11693
Scientific ReportsNature Publishing GroupYeshttp://www.nature.com/srep/index.html


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


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

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.

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

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

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://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/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

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

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/

Just for Fun

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 .

YouTube

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

Favorites

Favorite things of all kinds:

Bioinformatics blogs:

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

Personal tools