Contact Info

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 clinical microbiology	American Society for Microbiology	No	http://jcm.asm.org/
mBio	ASM	Yes	http://mbio.asm.org/
Methods	Elsevier	No	http://www.journals.elsevier.com/methods
Microbiology	SGM/HighWire Press	No	http://mic.sgmjournals.org/
Metabolic Engineering	Elsevier	Partial	http://www.journals.elsevier.com/metabolic-engineering/
Molecular Systems Biology	EMBO/Nature Publishing Group	Yes	http://www.nature.com/msb/index.html
PLOS Computational Biology	Public Library of Science	Yes	http://www.ploscompbiol.org/
PLOS Pathogens	PLOS	Yes	http://www.plospathogens.org/
Proceedings of the National Academy of Sciences	National Academy of Sciences	No	http://www.pnas.org/
Protein expression and purification	Elsevier	No	http://www.sciencedirect.com/science/journal/10465928
Genome Announcements	ASM	Yes	http://genomea.asm.org/
Futures	Elsevier	?	http://www.sciencedirect.com/science/journal/00163287
Microbial Cell Factories	BioMedCentral	Yes	http://www.microbialcellfactories.com/
Engineering Studies	Taylor & Francis	?	http://www.tandfonline.com/loi/test20
FEMS Microbiology Reviews			http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
Nature Biotechnology	Nature Publishing Group	No	http://www.nature.com/nbt/index.html
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
Molecular Genetics & Genomic Medicine	Wiley	Yes	http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
Biochemistry and Molecular Biology Education	Wiley	No	http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
Current opinion in chemical biology	Elsevier		http://www.sciencedirect.com/science/journal/13675931
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/

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/

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/

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.