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Revision as of 09:49, 3 May 2013
Contact Info
- Jarle Pahr
- Norwegian University of Science and Technology
jarlemag@stud.ntnu.no
Education
2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology
Research interests
- Omega-3/poly-unsaturated fatty acid biosynthesis
- Metabolic networks & Metabolic engineering
- Molecular genetics of lactate utilization in bacteria
- Bacterial stringent response
Notes
Projects
Organisms
Mesoplasma florum
http://openwetware.org/wiki/Mesoplasma_florum
http://partsregistry.org/Mesoplasma_florum
http://microbewiki.kenyon.edu/index.php/Mesoplasma_florum
http://www.broadinstitute.org/annotation/genome/mesoplasma_florum
M. florum genome-scale model: http://biomodels.caltech.edu/BMID000000141045
Rhodococcus opacus
http://www.broadinstitute.org/blog/creature-feature-rhodococcus-opacus-pd630 http://mic.sgmjournals.org/content/146/5/1143.full.pdf
B. subtilis
C. glutamicum
Lactobacillus bulgaricus
http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus
Interesting articles
Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen
Environmentally controlled invasion of cancer cells by engineered bacteria
Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Genetic programs constructed from layered logic gates in single cells
Research centres/labs
Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/
Cold Spring Harbor Laboratory: http://www.cshl.edu/
Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/
Insititute for Systems Biology: https://www.systemsbiology.org
Virginia Bioinformatics Institute: https://www.vbi.vt.edu/
European Bioinformatics Institute: http://www.ebi.ac.uk/
ATCC: http://www.lgcstandards-atcc.org/
European Molecular Biology Laboratory (EMBL): http://www.embl.de/
http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html
http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
Research programs/projects
Statseq: http://www2.ab.wur.nl/statseq/
Online learning
Portals:
MIT Open Courseware: http://ocw.mit.edu/index.htm
Specific courses:
Computational investing course: https://www.coursera.org/course/compinvesting1
Linear and discrete optimization course: https://www.coursera.org/course/linearopt
https://www.coursera.org/course/macroeconomics
Bioinformatics algorithms: https://www.coursera.org/course/bioinformatics
Financial Engineering: https://www.coursera.org/course/fe
A beginner's guide to irrational behavior: https://www.coursera.org/course/behavioralecon
Computational molecular evolution: https://www.coursera.org/course/molevol
https://www.coursera.org/course/netsysbio
Introduction to Systems Biology: https://www.coursera.org/course/sysbio
Language
Chinese
http://english.cntv.cn/learnchinese/
http://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://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:
Speaking:
SpeakGoodChinese: http://www.speakgoodchinese.org/
Synthetic Biology
Competitions and challenges:
http://www.ia-sb.eu/go/synthetic-biology/
LabGenius: www.labgeni.us
Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/
Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html
TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering: http://synthetic-biology.bbn.com/tasbe.html
Raytheon BBN Synthetic biology publications: http://synthetic-biology.bbn.com/pubs.html'
BBN Synthetic biology tools: https://synbiotools.bbn.com/
Biological part collections
https://biobricks.org/bpa/find-a-part/
DYI Bio/Citizen science
http://blogs.plos.org/citizensci/
DYI Bio Europe: http://www.diybio.eu/
Open PCR: http://openpcr.org/
www.indiebiotech.com
Ask a Biosafety expert: http://ask.diybio.org/
Public Laboratory: http://publiclaboratory.org/home
BOSSLAB: http://bosslab.org/
Science hideout: http://www.youtube.com/user/ScienceHideout
BiologiGaragen: http://biologigaragen.org/
http://haberlandt.blablablab.org/
Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs
Crowdfunding
Projects:
http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit
http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
Contract research services
https://www.scienceexchange.com/
Home experiments/projects
(Legality may vary depending on your location)
How to do a pGlo transformation: http://www.youtube.com/watch?v=sovDqqhQJx8
http://www.instructables.com/id/The-Light-Fountain-a-Bioluminescent-Hourglass/
http://cibt.bio.cornell.edu/workshops_and_summer_programs/0608alum/lumos.pdf
http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/%3Eprotocol
Art and Strategy
Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp
http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment
http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/
Personal genomics
http://www.genomesunzipped.org/
uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
http://www.personalgenomes.org/
Companies
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/
Cambrian Genomics: https://angel.co/cambrian-genomics http://cambriangenomics.com/
Suppliers
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/
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/
Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152
http://www.millipore.com/index.do
See also http://www.made-in-china.com/
Open Biotechnology: http://www.openbiotech.com/
http://www.metabion.com/home/index.php
http://www.sbsbio.com/english/dnahc.html
Useful links
Conferences
SBx.0: http://sb6.biobricks.org/
Advances in Genome Biology and Technology: http://agbt.org/about.html
Personal Genomes & Medical Genomics (PGMG) (Cold Spring Harbor Laboratories meeting).
Scientific challenges and competitions
CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/
Assemblathon
Variathon: http://bioinf.dimi.uniud.it/variathon
Alignathon
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/
Wiki sites
SNPedia.com
Discussion and communities
http://molecularbiology.forums.biotechniques.com/
DYI Bio Google Group: https://groups.google.com/forum/?fromgroups#!forum/diybio
http://www.americanbiotechnologist.com/blog/
BioStar - questions and answers on bioinformatics and genomics: http://www.biostars.org/
Biology.stackexchange.com: http://biology.stackexchange.com/
http://www.biology-online.org/
https://www.researchgate.net/topics/?nav=discussions
http://www.protocol-online.org/biology-forums/
Nature Protocols discussion forum: http://network.nature.com/groups/natureprotocols/forum/topics
http://www.reddit.com/r/labrats/
http://scienceboard.net/forum/default.asp
http://branch.com/g/level-headed-biotech
Apps
mPartsregistry: http://mpartsregistry.appspot.com
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
George Church: http://arep.med.harvard.edu/gmc/
Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html
Chris Voigt
Pallsson
Tom Knight
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
Journals
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/ | |
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 | |
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 |
Biotechniques: http://www.biotechniques.com/
Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727
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
Publication tools:
Reference management / Social bookmarking:
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
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
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.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
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
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://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/
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
Nuclei Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn
ProtLifePred protein lifetime calculator: http://protein-n-end-rule.leadhoster.com/
See also: http://2012.igem.org/User_talk:Jarlemag and http://2012.igem.org/Team:NTNU_Trondheim/Links
US National Human Genome Research Institute: http://www.genome.gov/
Codon table: http://en.wikipedia.org/wiki/DNA_codon_table
LaTeX lab book: http://openwetware.org/wiki/LabbookInLatex
Los Alamos Technical Reports collection: http://www.sciencemadness.org/lanldocs.html
The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home
NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/
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
Super awesome Sylvia: http://sylviashow.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/
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
Jobs
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://adamilab.msu.edu/evolve-and-conquer/
http://phylo.cs.mcgill.ca/ (publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031362)
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/