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 engineering for biofuels production
- Molecular genetics of lactate utilization in bacteria
- Metabolic networks
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
Useful links
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
The database of useful biological numbers
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
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/
QuickChange primer design script: http://sosnick.uchicago.edu/stuff/quickchanger.pl
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
