User:Jarle Pahr
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
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/
Synthetic Biology
DYI Bio/Citizen science
Open PCR: http://openpcr.org/
GenSpace: http://genspace.org/projects
www.indiebiotech.com
Ask a Biosafety expert: http://ask.diybio.org/
Personal genomics
http://www.genomesunzipped.org/
Companies
http://www.syntheticgenomics.com/
Suppliers
DongSheng Biotech: http://dongshengbio.com/en/index.asp
Macrogen Inc.: http://www.macrogen.com/eng/index/
Carolina Biological: http://www.carolina.com/
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/
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
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
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
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
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
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
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
Addgene restriction digest protocol: http://www.addgene.org/plasmid_protocols/restriction_digest/
http://www.methods.info/Methods/RNA_DNA/restr_analysis.html
http://www.methodbook.net/dna/restrdig.html
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
Science News
Publications
The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
SciTech Daily: http://scitechdaily.com/
The Scientis: http://www.the-scientist.com/
