From OpenWetWare

Journal name	Publisher	Open access status	Link
ACS Synthetic Biology	American Chemical Society	No	http://pubs.acs.org/journal/asbcd6
Bioengineered (Previously: Bioengineered bugs)	Landes Bioscience	Partial	http://dev.landesbioscience.com/journals/bioe/
Bioinformatics	Oxford Journals		http://bioinformatics.oxfordjournals.org/
BMC Medical Genomics	BMC	Yes	http://www.biomedcentral.com/bmcmedgenomics/
BMC Proceedings	BMC	Yes	http://www.biomedcentral.com/bmcproc
PLOS One	Public Library of Science	Yes	http://www.plosone.org/
Nucleic Acids Research	Oxford Journals	Yes	http://nar.oxfordjournals.org/
BMC Systems Biology	BioMedCentral	Yes	http://www.biomedcentral.com/bmcsystbiol/
BMC Microbiology	BioMedCentral	Yes	http://www.biomedcentral.com/bmcmicrobiol
Cell Reports	Cell Press	Yes	http://cellreports.cell.com/
The EMBO Journal	Nature Publishing Group	No	http://www.nature.com/emboj/index.html
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
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

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

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

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

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/

Super awesome Sylvia: http://sylviashow.com/

http://www.technologyreview.com/

http://www.scilogs.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/

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/

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

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

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

The PCR song: http://www.youtube.com/watch?v=x5yPkxCLads

Biorad GTCA song: http://www.youtube.com/watch?NR=1&feature=endscreen&v=ID6KY1QBR5s

iGEM style! http://www.youtube.com/watch?v=KHhswxo6xow

English Tea Time Gene: http://partsregistry.org/Part:BBa_J49005

Trust me, I'm an engineer: http://www.youtube.com/watch?v=rp8hvyjZWHs

I'm an Engineering failure: http://www.youtube.com/watch?v=ro3EPPYbn44

DNA text codec: http://www.sgidna.com/translator.php

Funny bioinformatic tool names: http://www.biostars.org/p/67874/

http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/

YouTube

Favorites

Favorite things of all kinds:

Bioinformatics blogs:

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

@@ Line 19: / Line 19: @@
 ==Notes==
-[[User:Jarle Pahr/Electrophoresis|Electrophoresis]]
+[[User:Jarle Pahr/Algorithms|Algorithms]]
+[[User:Jarle Pahr/Applications|Apps]]
+[[User:Jarle Pahr/16S_RNA|16S RNA]]
+[[User:Jarle Pahr/Biology|Biology]]
+[[User:Jarle Pahr/Biofilms|Biofilms]]
+[[User:Jarle Pahr/Bitesize|Bitesize Biology]]
+[[User:Jarle Pahr/BioBricks|BioBricks]]
+[[User:Jarle Pahr/Bioinformatics|Bioinformatics]]
+[[User:Jarpe Pahr/BAMBI|BAMBI]]
+[[User:Jarpe Pahr/BAMBI#BAMBI-LAST|BAMBI-LAST]]
+[[User:Jarpe Pahr/BAMBI#BAMBI-FAST|BAMBI-FAST]]
+[[User:Jarle Pahr/BLAST|BLAST]]
+[[User:Jarle Pahr/Books|Books]]
 [[User:Jarle Pahr/Buffers|Buffers]]
-[[User:Jarle Pahr/lablessons|Lab lessons]]
+[[User:Jarle Pahr/Calculations|Calculations]]
-[[User:Jarle Pahr/Restriction|Restriction]]
+[[User:Jarle Pahr/Centrifugation|Centrifugation]]
-[[User:Jarle Pahr/DNA|DNA]]
+[[User:Jarle Pahr/Checklists|Checklists]]
-[[User:Jarle Pahr/PCR|PCR]]
+[[User:Jarle Pahr/Chemicals|Chemicals]]
 [[User:Jarle Pahr/Cloning|Cloning]]
-[[User:Jarle Pahr/Vectors|Vectors]]
+[[User:Jarle Pahr/Computation|Computation]]
+[[User:Jarle Pahr/Control_theory|Control theory]]
+[[User:Jarle Pahr/Databases|Databases]]
+[[User:Jarle Pahr/DNA|DNA]]
+[[User:Jarle Pahr/Electrophoresis|Electrophoresis]]
+[[User:Jarle Pahr/Electronics|Electronics]]
+[[User:Jarle Pahr/Experiments|Experiments]]
+[[User:Jarle Pahr/Expression|Expression]]
+[[User:Jarle Pahr/Equipment|Equipment]]
+[[User:Jarle Pahr/Genes|Genes]]
+[[User:Jarle Pahr/Genetics|Genetics]]
+[[User:Jarle Pahr/Graph_theory|Graph theory]]
+[[User:Jarle Pahr/Growth_media|Growth media]]
+[[User:Jarle Pahr/Hardware|Hardware]]
+[[User:Jarle Pahr/iGEM|iGEM]]
+[[User:Jarle Pahr/lablessons|Lab lessons]]
 [[User:Jarle Pahr/Ligation|Ligation]]
-[[User:Jarle Pahr/Biology|Biology]]
+[[User:Jarle Pahr/Liquid_handling|Liquid handling]]
-[[User:Jarle Pahr/Transformation|Transformation]]
+[[User:Jarle Pahr/Microscopy|Microscopy]]
-[[User:Jarle Pahr/Books|Books]]
+[[User:Jarle Pahr/Models|Models]]
-[[User:Jarle Pahr/Questions|Research questions]]
+[[User:Jarle Pahr/Microbiology|Microbiology]]
+[[User:Jarle Pahr/Organisms|Organisms]]
+[[User:Jarle Pahr/Oligonucleotides|Oligonucleotides]]
+[[User:Jarle Pahr/Simulations|Simulations]]
+[[User:Jarle Pahr/Open_science|Open science]]
+[[User:Jarle Pahr/Patents|Patents]]
+[[User:Jarle Pahr/Persistence|Persistence]]
+[[User:Jarle Pahr/Plasmids|Plasmids]]
+[[User:Jarle Pahr/Phylogenetics|Phylogenetics]]
+[[User:Jarle Pahr/Promoters|Promoters]]
+[[User:Jarle Pahr/Protocols|Protocols]]
+[[User:Jarle Pahr/PCR|PCR]]
 [[User:Jarle Pahr/Programming|Programming]]
+[[User:Jarle Pahr/Refuted|Refuted]]
+[[User:Jarle Pahr/Robotics|Robotics]]
+[[User:Jarle Pahr/Questions|Research questions]]
+[[User:Jarle Pahr/Recipes|Recipes]]
+[[User:Jarle Pahr/Restriction|Restriction]]
+[[User:Jarle Pahr/RNA|RNA]]
+[[User:Jarle Pahr/Safety|Safety]]
 [[User:Jarle Pahr/Software|Software]]
-[[User:Jarle Pahr/Hardware|Hardware]]
+[[User:Jarle Pahr/Statistics|Statistics]]
-[[User:Jarle Pahr/iGEM|iGEM]]
+[[User:Jarle Pahr/Sterilization|Sterilization]]
-[[User:Jarle Pahr/Bioinformatics|Bioinformatics]]
+[[User:Jarle Pahr/Synthetic_biology|Synthetic Biology]]
+[[User:Jarle Pahr/Systems_biology|Systems Biology]]
+[[User:Jarle Pahr/Transformation|Transformation]]
+[[User:Jarle Pahr/Vectors|Vectors]]
+[[User:Jarle Pahr/Vectors|Verification]]
 ==Projects==
@@ Line 60: / Line 158: @@
 ==Organisms==
+===Escherichia coli===
 ===Mesoplasma florum===
@@ Line 82: / Line 184: @@
 ===Lactobacillus bulgaricus===
 http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus
 ==Interesting articles==
@@ Line 111: / Line 211: @@
 ATCC: http://www.lgcstandards-atcc.org/
+European Molecular Biology Laboratory (EMBL): http://www.embl.de/
 http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html
+http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
 ==Research programs/projects==
@@ Line 118: / Line 222: @@
 Statseq: http://www2.ab.wur.nl/statseq/
-==Online courses==
+==Online learning==
+'''Portals:'''
+http://www.class-central.com/
+http://www.core.org.cn
 https://www.coursera.org/
@@ Line 125: / Line 234: @@
 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
@@ Line 143: / Line 259: @@
 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/
@@ Line 171: / Line 367: @@
 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://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/
@@ Line 210: / Line 434: @@
 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===
+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/
@@ Line 223: / Line 484: @@
 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==
@@ Line 261: / Line 527: @@
 http://www.nucleics.com/
+https://www.transcriptic.com/
-Cambrian Genomics: https://angel.co/cambrian-genomics
+Cambrian Genomics:
+https://angel.co/cambrian-genomics
+http://cambriangenomics.com/
+http://www.genologics.com
 ==Suppliers==
+BioBasic: http://store.biobasic.com/
 Promega: http://no.promega.com/
@@ Line 289: / Line 562: @@
 Jena BioScience: http://www.jenabioscience.com/
+http://www.synthesisgene.com/
 Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152
@@ Line 297: / Line 572: @@
 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.iorodeo.com/
+'''Used equipment vendors:'''
+http://www.labrecyclers.com/index.html
 ==Useful links==
 *[[OpenWetWare:Welcome|Introductory tutorial]]
 *[[Help|OpenWetWare help pages]]
+===Conferences and meetings===
+'''Synthetic Biology:'''
+SBx.0: http://sb6.biobricks.org/
+Applications for Synthetic Biology in Industrial Biotechnology 2013: http://www.clocate.com/conference/Applications-for-Synthetic-Biology-in-Industrial-Biotechnology-2013/38757/
+'''Genomics:'''
+Advances in Genome Biology and Technology: http://agbt.org/about.html
+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
 ===Educational resources===
@@ Line 312: / Line 652: @@
 https://www.manylabs.org/
+=Wiki sites=
+http://www.scholarpedia.org
+SNPedia.com
+http://www.wikigenes.org
+http://ecoliwiki.net
 ===Discussion and communities===
@@ Line 334: / Line 685: @@
 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===
@@ Line 340: / Line 699: @@
 ===Persons/Research groups===
+Jim Collins: http://www.bu.edu/abl/
+Jason Kelly: http://openwetware.org/wiki/Jason_Kelly
 Tom Ellis: http://openwetware.org/wiki/User:Ellis
@@ Line 345: / Line 708: @@
 George Church: http://arep.med.harvard.edu/gmc/
-Jay Keasling
+Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html
 Chris Voigt
@@ Line 352: / Line 715: @@
 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
@@ Line 361: / Line 727: @@
 Jean Peccoud
-===Journals===
+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
+===Publications===
@@ Line 371: / Line 759: @@
 |-
 | Bioengineered (Previously: Bioengineered bugs) || Landes Bioscience ||Partial ||http://dev.landesbioscience.com/journals/bioe/
+|-
+|Bioinformatics||Oxford Journals|| ||http://bioinformatics.oxfordjournals.org/
+|-
+|BMC Medical Genomics||BMC||Yes||http://www.biomedcentral.com/bmcmedgenomics/
+|-
+|BMC Proceedings||BMC||Yes||http://www.biomedcentral.com/bmcproc
 |-
 | PLOS One  ||Public Library of Science || Yes ||http://www.plosone.org/
@@ Line 379: / Line 773: @@
 |-
 |BMC Microbiology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcmicrobiol
+|-
+|Cell Reports||Cell Press ||Yes||http://cellreports.cell.com/
 |-
 |The EMBO Journal||Nature Publishing Group ||No||http://www.nature.com/emboj/index.html
 |-
 |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/
@@ Line 407: / Line 805: @@
 |-
 |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
+|-
+|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
 |}
+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/
@@ Line 418: / Line 846: @@
 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===
@@ Line 464: / Line 910: @@
 GenBank
+http://datadryad.org/
+http://www.cathdb.info/
 ===Codon usage===
@@ Line 491: / Line 941: @@
 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===
@@ Line 553: / Line 1,013: @@
 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:
@@ Line 637: / Line 1,099: @@
 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/#
@@ Line 713: / Line 1,178: @@
 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. ====
@@ Line 725: / Line 1,196: @@
 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
@@ Line 745: / Line 1,218: @@
 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
-====Science News ====
+https://genomeinterpretation.org
+===Science News ===
-===Magazines/Blogs===
+===Magazines/Blogs/Newssites===
 The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
@@ Line 765: / Line 1,244: @@
 http://www.reportergene.com/
+Super awesome Sylvia: http://sylviashow.com/
+http://www.technologyreview.com/
+http://www.scilogs.com/
+'''Blogs:'''
 http://retractionwatch.wordpress.com/
@@ Line 771: / Line 1,258: @@
 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/
+Social media:
+http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
 ===In the news/Commentaries===
@@ Line 781: / Line 1,292: @@
 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
+===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===
@@ Line 795: / Line 1,340: @@
 I'm an Engineering failure: http://www.youtube.com/watch?v=ro3EPPYbn44
+DNA text codec: http://www.sgidna.com/translator.php
+Funny bioinformatic tool names: http://www.biostars.org/p/67874/
+http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/
+=YouTube=
+=Favorites=
+Favorite things of all kinds:
+Bioinformatics blogs:
+http://www.homolog.us/blogs/

User:Jarle Pahr

From OpenWetWare

Current revision

Contents

Contact Info

Education

Research interests

Notes

Projects

Organisms

Escherichia coli

Mesoplasma florum

Rhodococcus opacus

B. subtilis

C. glutamicum

Lactobacillus bulgaricus

Interesting articles

Research centres/labs

Research programs/projects

Online learning

Language

Chinese

Synthetic Biology

Biological part collections

DYI Bio/Citizen science

Crowdfunding

Contract research services

Home experiments/projects

Art and Strategy

Personal genomics

Companies

Suppliers

Useful links

Conferences and meetings

Scientific challenges and competitions

Educational resources

Wiki sites

Discussion and communities

Apps

Persons/Research groups

Publications