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Univ of Manchester | MIB | Genomics | Proteomics | Transcriptomics | Metabolomics | Systems Biology | Molecular Biology | Bioscience Departments | BioImaging

Functional Categories for Functional Genomics | Network Science | Genetic Programming and Evolutionary Computing Links

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University of Manchester

UoM - Chemistry - All Academic Depts - Manchester Uni Search page - Manchester Café Scientifique - Manchester Informatics -
Webmail - MAIL ACCOUNT MANAGER -
JRUL e-journals A-Z -
Metabolomics2007 -



MIB  (Manchester Interdisciplinary Biocentre)

MIB website


General Links

BBSRC - (BBSRC 10-yr vision) (BBSRC CISB) (Bioenergy review) - Webmail - DRINC - EPSRC - European Research CouncilNERC (forms) - MRC - MRC EAA - RCUK - RS and e-GAP system - Wellcome - Cheminformatics Wiki - grantsnet.co.ukGrantsnet.org - HEFC - HERO UK Univ portal - RAE - OST - Je-S system - OASISSTFC and its Science Board - UKBiobank -

Campaign for Science & Engineering (ex-SBS) - CPGS and 2008 meeting - DOI resolver - Northwest Science - Met-RO - Lambert Agreements - Metabolomics phase 2 - National Centre for Text Mining - Funding opportunities - EPS ResearchEPS Research FAQs - UKMT -
Journals: ChemJournals - ACS - Anal Chem - Bioinformatics - Chemolab - J.Biomol.Screening - JCS Perkin I - Nature - PNAS - Science -

Courses: MIT OpenCourseWare -

Bibliographic: AnatomyLens - Arrowsmith - Citeseer - CiteULike - Connotea - Duncan's older blog - Duncan's newer blog and lablog - ESI - ETBLAST - Google Scholar - GOPUBMEDHubmed - Journal Citation Reports - NIH grants search toolOther TM tools at Arrowsmith - PathBinderH - Pubchem - Pubmed - Scimago - Scopus - UKPubMedCentral - WoK -

 

Cheminformatics: - our wiki - dynamic SMILES -

 

Grant finding toolsNIH grants search tool  - UKPMC Grant Lookup Tool -

 

Search Engines: Google - Dogpile - MSN search - Clusty - Manchester Uni Directory -

 

Analytical Portals: ASDLib - CE&CEC -

 

Grid/Web: BioWeb Services - myExperiment - myGrid - ONDEX Wiki - ProgrammableWeb - Taverna - UTOPIA -     

 

Conferences: ICSB2007 - SAMO2007 -

 

MS Windows update - MS Office update -

Maps: Google maps - MS Live maps - Multi Media Mapping - UK Street Map -
USNO Master Clock or World Timeserver

World Travel Guide - by Columbus Internet
Association of National Tourist Organisations - world wide
Met Office Weather pages for NW - Met Office Weather pages for Aberystwyth

BBC Weather pages for Manchester Aberystwyth - Oswestry - Wrexham -
Currency Exchange Rates from xe - from Aquariussoft -
Eurocompass Guide for the Independent Traveller
Weather & Climate - including up to 10 day forecasts worldwide

Finite Improbability Calculator
Instructions to Authors for all journals


Free animated gif files: WilsonInfo



Genomics

DBCAT - Encyclopedia of Life project - Genomics Glossaries, Y.F. Leung's Functional Genomics Portal, Pedro's Biomolecular Research Tools, Omegabase Sequences and more - portals for all things biological, -Omes Glossary.

EBI Genome Monitor, EMGL, Genamics, GOLD, Prominent Organisms at NCBI, ORNL, TIGR Microbial Database - indexes of genome sequences.

Nature Genomics Gateway.

E. coli: COG at NCBI, Colibri Web Server, ECDC E. coli Database Collection (Gießen), Ecogene (Kenn Rudd), Ecocyc, Genobase (Nara, Japan), Genome Navigator (Dahlem), IECA PortalMIPS/PEDANT.

M. tuberculosis: H37Rv (Sanger), MIPS/PEDANT, Tuberculist.

S. cerevisiae: MIPS/PEDANT, Stanford Genome Database, MIPS CYGD, Yale Genome Analysis Center, YPD.

S. coelicolor: A3(2) at Sanger, IGF homepage, UMIST Microarray Resource, Proteome Reference Gel


Proteomics

2D gel electrophoresis tutorial in Aber

Expasy - home page and portal for many proteomics tools, including World 2D PAGE list and Protocols for 2D-PAGE

Catalogue of 2D gel pages on the Web

HUMAN PROTEIN ATLAS

Mutliident - lots of ways of checking out proteins

PROWL - a resource for protein chemistry and mass spectrometry (and a good one for peptide mass fingerpriting)

Protein Prospector, PepSea, MOWSE, MASCOT, PepFrag, (other good ones for peptide mass fingerprinting)

Proteome, Inc - a commercial venture with good yeast and worm proteomics

Profound - Bayesian system for peptide mass fingerprinting vs NIH nr database.

Proteome gel software: PDQuest, Melanie, Phoretics.



Transcriptomics

HUMAN TRANSCRIPTOME PROFILES -

Labs: Pat Brown (Stanford), Leroy Hood Lab (Seattle), Vivian Cheung (Phildelphia), EBI arrayexpress , AECOM, Ontario Cancer Institute, Rick Young (Whitehead),

Chip and Microarray Companies: Affymetrix, Agilent, AmershamPharmacia Biotech, Arrayit, Axon Instruments Genepix, Biorobotics, Clontech (Atlas Arrays), Eurogentec, Corning CMT, GeneLogic GeneExpress, Genomic Solutions, GSI Lumonics ScanArray, Iobion Genetraffic, Mergen ExpressChip, Microarrays.org Public Database, Oxford Gene Technology, Origene RapidScan, Research Genetics, Stratagene Gene Connection,

Companies Providing Bioinformatics Tools: BioDiscovery Genesight, Gene Data GD Expressionist, Genedata, GeneLogic Gene Express, Incyte, Lion Bioscience AG Array Scout, Research Genetics, Rosetta Resolver, Silicon Genetics Gene Spring.

Analysis Groups: Aberystwyth, Manchester, Whitehead/MIT, Stanford, NHGRI/NIH Microarray Project.

Data, Ontologies and Standards: Array XML working group MGED project, DAML, EBI Array Express, GenePix File Formats, MaxD, NCGR GeneX, NCBI Gene Expression Omnibus, Working Recommendations on Standards, MAGE-ML.

'Free' software (sometimes free only for non-commercial use) on the Web: EBI Expression Profiler, Michael Eisen's Clustering Software, MaxD View, TIGR Array Viewer, TM4 including Multi-Experiment Viewer.

Portals: Microarray Data, Papers and Links at the Rockefeller, Links from the EBI, Many Transcriptomic Links at Deathstar, Inc., Microarray Software Links at Stanford, Microarray Software Comparisons by Yuk Fai Leung, Microarrays.org.



Metabolomics

Links for metabolomics are via our Metabolomics Homepage


Systems Biology

Links for Systems Biology are via our Systems Biology Homepage


Molecular Biology

A Guide to Molecular Sequence Analysis, Pedro's Biomolecular Research Tools, Biopolymer Markup Language.


Bioscience Departments

Biotutor - quick link to all UK Bioscience Departments


BioImaging

Amersham IN Cell Analyser, Cellomics ArrayScan, Evotec Opera.

Bioimage.org, Open Microscopy Environment.


Functional Categories for Functional Genomics

If the functional genomics agenda is to assign function or functional class to genes of unknown function, it is necessary to have a list of the classes to which one might wish to assign them. The following therefore lists some websites in which a listing of suggested functional classes has been given.

Organism URL


Bacillus subtilis

http://bioweb.pasteur.fr/GenoList/SubtiList/help/classif-search.html

Caenorhabditis elegans

http://www.proteome.com/databases/WormPD/WormPDcategories/
Functional_Categories.html

Escherichia coli

http://ecocyc.pangeasystems.com/ecocyc/ecocyc.html
http://www.genome.ad.jp/dbget-bin/get_htext?E.coli.operon.kegg

Mycobacterium tuberculosis

http://www.sanger.ac.uk/Projects/M_tuberculosis/Gene_list

Saccharomyces cerevisiae

http://www.mips.biochem.mpg.de/proj/yeast/catalogues/funcat/index.html
http://www.proteome.com/databases/YPD/YPDcategories/
Functional_Categories.html

Note that many of these classification structures are are strictly hierarchical and are far from optimal. See Kell, D.B. & King, R.D. (2000) On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning. Trends Biotechnol. 18, 93-98. Pubmed abstract. The goal of the Gene Ontology consortium is to bring order and a systematic structure to these terms. Another comparison of functional annotation schemes has been published by SCG Rison, TC Hodgman & JM Thornton (2000) Functional and Integrative Genomics 1, 56-69 - see link here and a Table of links to other functional catalogues.


Network Science

Some properties of networks are generic, and we need tools to study and understand them. Links to these are on our Systems Biology page.



Genetic Programming and Evolutionary Computing Links

Very much under construction...

People: John Koza's Homepage

Bibliographic: The GP bibliography, Bibliography on GP

Tutorials: Genetic Programming FAQs, GP Tutorial at GeneticProgramming.com, GP Tutorial at Stanford.

Hardware: Adrian Stoica JPL, Anadigm, Xilinx.

Software: Academic, Commercial, Aber Genomic Computing.

Other Overviews: Genetic Programming.org, Cluster Computing Links, Evonet.
 
Other Links

Many thanks to Iolo for a lot of these...

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Last update: 27th July 2012


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