User:Jarle Pahr

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/
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
The EMBO Journal	Nature Publishing Group	No	http://www.nature.com/emboj/index.html
Genome Research	Cold Spring Harbor Press	Partial (6 month embargo)	http://genome.cshlp.org/
Genome Medicine	BioMedCentral	Yes	http://genomemedicine.com/
Journal of molecular biology	Elsevier	Partial	http://www.journals.elsevier.com/journal-of-molecular-biology/
Journal of biological chemistry	American Society for Biochemistry and Molecular Biology.	No	http://www.jbc.org/
Journal of bacteriology	American Society for Microbiology	No	http://jb.asm.org/
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/
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
Journal of Computational Biology	Liebert Publishing	No	http://www.liebertpub.com/CMB

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

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

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/

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://www.doaj.org/

Publication tools:

https://collage.elsevier.com/

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

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.

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

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

Magazines/Blogs/Newssites

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

SciTech Daily: http://scitechdaily.com/

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

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

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

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

http://www.reportergene.com/

http://www.technologyreview.com/

Blogs:

http://retractionwatch.wordpress.com/

http://www.genomesunzipped.org/

http://ing.dk/blogs/folkeforsker

http://phylogenomics.blogspot.no/

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

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

http://dienekes.blogspot.no/

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

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

Social media:

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

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