Handy Links

Univ of Manchester | MIB | Genomics | Proteomics | Transcriptomics | Metabolomics | Systems Biology | Molecular Biology | Bioscience Departments | BioImagingFunctional Categories for Functional Genomics | Network Science | Genetic Programming and Evolutionary Computing Links General Links | Rail Travel | Ferries etc. | Air Travel | Travel Agents/Hotels etc. | Road Travel/Cars etc. | Aberystwyth | Chirk | London | Manchester | Swindon | Fun
University of Manchester
UoMChemistryManchester Uni Search pageManchester Café ScientifiqueManchester InformaticsWebmailJRUL e-journals A-ZMetabolomics2007

MIB  (Manchester Interdisciplinary Biocentre)
MIB website

General Links
BBSRC(BBSRC 10-yr vision) (BBSRC CISB) (Bioenergy review) – WebmailDRINCEPSRCEuropean Research Council –  NERC (forms) – MRCRCUKRS and e-GAP systemWellcome – grantsnet.co.uk –  Grantsnet.orgHEFC –  REF GOSJe-S system –   STFC and its Science BoardUKBiobank

Campaign for Science & Engineering (ex-SBS)CPGS and 2008 meetingDOI resolverNorthwest ScienceMet-ROLambert AgreementsMetabolomics phase 2National Centre for Text MiningFunding opportunitiesEPS Research –  EPS Research FAQsUKMT Journals: ChemJournalsACSAnal ChemBioinformaticsChemolab J.Biomol.ScreeningJCS Perkin INaturePNASScience

Courses: MIT OpenCourseWare

Bibliographic: AnatomyLensArrowsmithCiteseerCiteULikeConnoteaDuncan’s older blogDuncan’s newer blog and lablogESIETBLASTGoogle ScholarGOPUBMED –  HubmedJournal Citation ReportsNIH grants search tool –  Other TM tools at ArrowsmithPathBinderHPubchemPubmedScimagoScopusUKPubMedCentralWoK

Cheminformatics: – dynamic SMILES

Grant finding toolsNIH grants search tool  – UKPMC Grant Lookup Tool

Search Engines: GoogleDogpileMSN search ClustyManchester Uni Directory

Analytical Portals: ASDLibCE&CEC

Grid/Web: BioWeb Services myExperiment myGridONDEX WikiProgrammableWebTavernaUTOPIA

Conferences: ICSB2007SAMO2007

MS Windows update Info

Maps: Google mapsMS Live mapsMulti Media MappingUK 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 NWMet Office Weather pages for Aberystwyth

BBC Weather pages for Manchester –  Aberystwyth OswestryWrexhamCurrency Exchange Rates from xe from AquariussoftEurocompass 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

DBCATEncyclopedia of Life projectGenomics 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 Portal –  MIPS/PEDANT.

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

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

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

2D gel electrophoresis tutorial in AberExpasy – 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


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.

HUMAN TRANSCRIPTOME PROFILESLabs: 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.

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

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… Rail Travel

Ferries etc.

Air Travel

Travel Agents/Hotels etc.

Road Travel/Cars etc.