User:Jarle Pahr: Difference between revisions
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Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs | |||
==Art and Strategy== | ==Art and Strategy== |
Revision as of 09:54, 16 February 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/
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
DYI Bio/Citizen science
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
Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs
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
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/
Suppliers
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
Books
Gene Synthesis: http://link.springer.com/book/10.1007/978-1-61779-564-0/page/1
Useful links
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/
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/
Persons
Tom Ellis: http://openwetware.org/wiki/User:Ellis
George Church: http://arep.med.harvard.edu/gmc/
Jay Keasling
Chris Voigt
Pallsson
Tom Knight
Drew Endy: http://openwetware.org/wiki/User:Endy
Journals
Bioengineered (Previously: Bioengineered bugs): http://dev.landesbioscience.com/journals/bioe/
Metabolic Engineering: http://www.journals.elsevier.com/metabolic-engineering/
PLOS One: http://nar.oxfordjournals.org/
BMC Systems Biology: http://www.biomedcentral.com/bmcsystbiol/
Molecular Systems Biology: http://www.nature.com/msb/index.html
BMC Microbiology
PLOS Computational Biology: PLOS Computational Biology
Proceedings of the National Academy of Sciences: http://www.pnas.org/
Journal of molecular biology:
Journal of biological chemistry:
Journal of bacteriology
The EMBO Journal
ACS Synthetic Biology: http://pubs.acs.org/journal/asbcd6
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
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/
Programming
BioPython: http://biopython.org/wiki/Main_Page
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
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
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
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
Protocols
OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols
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
Protocol online: http://protocol-online.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
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
Science News
Magazines/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/
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
In the news
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