User:Jarle Pahr

Contact Info

Jarle Pahr (an artistic interpretation)

• Jarle Pahr
• Norwegian University of Science and Technology

jarlemag@stud.ntnu.no

• Email me through OpenWetWare

Education

2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology

Research interests

1. Omega-3/poly-unsaturated fatty acid biosynthesis
2. Metabolic networks & Metabolic engineering
3. Molecular genetics of lactate utilization in bacteria
4. Bacterial stringent response

Notes

Electrophoresis

Lab lessons

Restriction

DNA

PCR

Transformation

Projects

ppGpp MSc. project

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

http://bsubcyc.org/

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

http://www.synbioproject.org/

http://www.synbiont.org/

Competitions and challenges:

http://igem.org

http://genocon.org/

http://www.ia-sb.eu/go/synthetic-biology/

LabGenius: www.labgeni.us

http://synbio.org.uk/

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

http://diybioftw.com/

http://dyibio.org

DYI Bio Europe: http://www.diybio.eu/

http://genefoo.com/

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/

http://biocurious.org/

http://genspace.org/

Science hideout: http://www.youtube.com/user/ScienceHideout

http://basementbiotech.org/

http://www.biotinker.com/

Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs

Programming

Beginning Python fro bioinformatics Wiki: http://wiki.genedrift.org/doku.php?id=beginning_python_for_bioinformatics

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

https://www.23andme.com/

http://www.23andyou.com

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/

http://www.labsupplymall.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

http://www.dummies.com/store/product/Bioinformatics-For-Dummies-2nd-Edition.productCd-0470089857.html

Useful links

• Introductory tutorial
• OpenWetWare help pages

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/

BioStar - questions and answers on bioinformatics and genomics: http://www.biostars.org/

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

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/

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

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

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://insilico.ehu.es/PCR/

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

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

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