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July 31, 2006
Resources for Omics Researchers (Omics Series, 16)
While there are a great many resources for omics researchers, both in print and online, these change rapidly and unpredictably, as do the field themselves. Today's entry includes protocols, open-source software, and a few general collections of research resources in these areas. In addition to the resources listed here (all of which were good links as of July 2006), remember to also check the website for the company that produced your equipment, as many corporations also provide detailed protocols guides.
* ONLINE RESOURCES
ApoptosisWorld, resources for studying cell death: http://www.apoptosisworld.com/
BioDAS (Biological Distributed Annotation System): http://biodas.org/
"This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data."
Bioinformatics.Org: The Open-Access Institute: http://bioinformatics.org/
CPAS: http://cpas.fhcrc.org/
"CPAS is an open source science portal offering web-based bioinformatics and collaboration tools to help scientists store, analyze, and share data from high-throughput experiments and clinical trials. The Fred Hutchinson Cancer Research Center uses CPAS to manage the Computational Proteomics Laboratory (CPL) Proteomics Repository containing over 140 million putative MS2 peptides, growing at 3 million per week. CPAS is available as free, installable software, with source code."
Drug Discovery & Development: Buyer's Guide: http://www.dddmag.com/BuyersGuide.aspx
GenomicWorld, resources for genomics and genetics: http://www.genomicworld.com/
Ion Channel Group: Bioinformatics, Databases and Software for Medicine: http://www.bio-computing.org/
Includes: "The first & only bioinformatics-specific relevancy-powered MEDLINE search." "Hint: Sort by citation score to display the highest impact articles."
Max-Planck-Institute of Immunobiology: Proteomics Protocols: http://www.immunbio.mpg.de/home/facilities/proteomics/protocols/index2.html
MicroarrayWorld, resources for microarrays and expression profiling: http://www.microarrayworld.com/
Molecular Station: Links: Proteomics Protocols: http://www.molecularstation.com/protocol-links/Proteomics_Protocols/
Molecular Station: Molecular Biology Techniques: http://www.molecularstation.com/molecular-biology-techniques/
Molecular Station: Proteomics Protocols: http://www.molecularstation.com/proteomics/proteomics-protocols/
msInspect: http://proteomics.fhcrc.org/CPL/msinspect.html
"msInspect allows you to view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration."
ProteomicWorld: http://www.proteomicworld.org/
Includes: instruments, protocols, reagents, protein arrays, software, databases and more.
Protocol Online: Index to Protocols: http://www.protocol-online.org/prot/
Sashimi: http://sashimi.sourceforge.net/
"The goal of the project is to provide the scientific community with free open source software tools for the downstream analysis of mass spectrometric data. We hope to develop and distribute analysis tools that will facilitate the ability of labs worldwide to perform proteomics experiments."
* BOOKS IN DENTISTRY LIBRARY
For additional books on this topic, we highly recommend the Science Library and Taubman Medical Library.
Cell cycle control and dysregulation protocols : cyclins, cyclin-dependent kinases, and other factors / edited by Antonio Giordano, Gaetano Romano. QH 605 .C42571 2004
Cytokine protocols / edited by Marc de Ley. QH 506 .M451 v.249
Protein purification protocols. QP 551 .P697561 2004
Recombinant gene expression : reviews and protocols / edited by Paulina Balbás and Argelia Lorence. QH 443 .R361 2004
Short protocols in cell biology : a compendium of methods from Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]. QH 585.2 .S55 2004
Bone research protocols / edited by Miep H. Helfrich, Stuart H. Ralston. QP 88.2 .B58981 2003
PCR protocols / edited by John M.S. Bartlett and David Stirling. QP 606 .D46 P35951 2003
Protein sequencing protocols / edited by Bryan John Smith. QP 625 .N89 P761 2002
* WANT MORE?
Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (instruments OR protocols OR reagents OR "open source")
Posted by pfa at July 31, 2006 12:48 PM