Latest revision as of 15:47, 27 July 2016

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/

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/

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.

@@ Line 1: / Line 1: @@
 ==Contact Info==
-[[Image:OWWEmblem.png|thumb|right|Jarle Pahr (an artistic interpretation)]]
+[[Image:JPA.jpeg|thumb|right|Jarle Pahr]]
 *Jarle Pahr
-*Norwegian University of Science and Technology
+jarlemag@alumni.ntnu.no
-jarlemag@stud.ntnu.no
 *[[Special:Emailuser/Jarle Pahr|Email me through OpenWetWare]]
@@ Line 10: / Line 9: @@
 -2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology
-==Research interests==
-<!-- Feel free to add brief descriptions to your research interests as well -->
+==Notes==
-# Omega-3/poly-unsaturated fatty acid biosynthesis
-# Metabolic engineering for biofuels production
-# Molecular genetics of lactate utilization in bacteria
+See [[User:Jarle Pahr/Notes|Notes]]
-#Metabolic networks
-#Bacterial stringent response
+==Projects==
+[[User:Jarle Pahr/Notebook/ppGpp Msc|ppGpp MSc. project]]
+==Organisms==
+See [[User:Jarle Pahr/Organisms|Organisms]]
 ==Interesting articles==
@@ Line 29: / Line 35: @@
 [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11516.html 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==
+See [[User:Jarle Pahr/Online_learning|Online learning]]
+==Language==
+==Synthetic Biology==
+See [[User:Jarle Pahr/Synthetic_biology|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 [[User:Jarle Pahr/DIYBio|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/
+<strike>http://www.labsupplymall.com/</strike>
+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/
+<strike>Open Biotechnology: http://www.openbiotech.com/</strike>
+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==
@@ Line 36: / Line 236: @@
 *[[Help|OpenWetWare help pages]]
+===Conferences and meetings===
+See [[User:Jarle Pahr/Conferences|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===
+{| 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===
@@ Line 50: / Line 603: @@
 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
+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
@@ Line 79: / Line 754: @@
 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
-====Bioinformatics & Annotation====
+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
@@ Line 96: / Line 778: @@
 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====
+===Cloning & Construction===
 The Constructor: http://2011.igem.org/Team:Wageningen_UR/Softwaretool/
@@ Line 109: / Line 812: @@
 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
@@ Line 124: / Line 927: @@
 The Oligator: http://gcat.davidson.edu/igem10/tutorial.html
-Nuclei Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
+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
@@ Line 131: / Line 936: @@
 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.

User:Jarle Pahr: Difference between revisions

Latest revision as of 15:47, 27 July 2016

Contact Info

Education

Notes

Projects

Organisms

Interesting articles

Research centres/labs

Research programs/projects

Online learning

Language

Synthetic Biology

Biological part collections

DIY Bio/Citizen science

Art and Strategy

Personal genomics

Companies

Suppliers

Useful links

Conferences and meetings

Scientific challenges and competitions

Resources for researchers

Educational resources

Wiki sites

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