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August 16, 2006
Staying Current: Omics Blogs & More (Omics Series, 23)
Assuming we already know that scientists prefer to get information from their peers, wouldn't it be great to be able to get it without even asking? Enter the blog.
Science blogs have become force to be reckoned with in the research information environment. Blogs may be from individuals (faculty, researchers, grad students) or from organizations (journals, corporations, newswires). The better science blogs define a topic they will focus on and rarely diverge from that. Many of the best blogs will also link to the other influential blogs on the same topic. These communities of bloggers are what has become known as the blogosphere.
In this blog entry, we highlight a few of the most influential or innovative blogs in several omics topics, following this with examples of sources and techniques for discovering additional blogs.
* GENOMICS
The BioTech Weblog: The -Omics Series, Part 1: Genomics: http://www.biotech-weblog.com/50226711/the_omics_series_part_1_genomics.php
DNA direct talk: Your DNA, Your Health, Your Choices: http://talk.dnadirect.com/
Genetics and Health (Hsien Hsien Lei, Ph.D.): http://www.geneticsandhealth.com/
MedBioWorld: Post-Genomics, Forging a Connection Between Research and Clinical Applications: http://www.medbioworld.com/postgenomics_blog/
Mendel's Garden: http://mendels-garden.blogspot.com/
The Personal Genome, Genomics as a medical tool and lifestyle choice: http://www.thepersonalgenome.com/
What's Next in Health: Category: Gene Research: http://www.whatsnextnetwork.com/health/index.php?cat=61
* PROTEOMICS
Comparative Proteomics: http://www.comparativeproteomics.org/
Genomics proteomics: http://genomics-proteomics.biotechnewstoday.com/
myProteome.com, The Proteomics IT Blog: http://www.myproteome.com/
Proteome Commons: http://www.proteomecommons.org/archive.jsp
Proteome Measures: http://proteomemeasures.blogspot.com/
* BIOINFORMATICS
Biological Computations: http://bifo.livejournal.com/
Biological Informatics: http://biologicalinformatics.blogspot.com/
Bionuz: Latest Bioinformatics News: http://bionuz.blogspot.com/
Flags and Lollipops - Bioinformatics & Genomics News and Views: http://www.ghastlyfop.com/blog
HubLog: http://hublog.hubmed.org/
Inforbiomatica: http://moseshohman.com/blog/
NodalPoint (A Bioinformatics Weblog): http://www.nodalpoint.org/
Notes from the Biomass: http://nftb.net/
Propellor Twist, RNA & Bioinformatics research and other interests: http://fjossinet.u-strasbg.fr/
What You're Doing is Rather Desperate: Bioinformatics: http://nsaunders.wordpress.com/tag/bioinformatics/
* NANOTECHNOLOGY
Advanced Nanotechnology (Brian Wang): http://advancednano.blogspot.com/
Foresight: Nanodot, the original nanotechnology weblog: http://www.foresight.org/nanodot/
nano | public, a weblog of nanotechnology and its impact on the public (Dietram A. Scheufele): http://nanopublic.blogspot.com/
Responsible Nanotechnology (World Care): http://crnano.typepad.com/crnblog
* OTHER RECOMMENDED SCIENCE & OMIC BLOGS
Aetiology: http://scienceblogs.com/aetiology/
The Biotech Weblog: http://www.biotech-weblog.com/
Discovering Biology in a Digital World: http://scienceblogs.com/digitalbio/
MedGadget, Internet Journal of Emerging Medical Technologies: http://www.medgadget.com/
The Omics World: http://harijay.wordpress.com/
The Scientific Activitist, Reporting from the Crossroads of Science and Politics: http://scienceblogs.com/scientificactivist/
Science Blogs: http://scienceblogs.com/
Institute for Ethics and Emerging Technologies: Ethical Technology Blog: http://ieet.org/index.php/IEET/IEETblog
* SEARCHING FOR BLOGS ON A TOPIC
Technorati Blog Finder: Genomics: http://www.technorati.com/blogs/genomics
Mendel's Garden #2: The Best of Genetics Blogging (By Hsien Hsien Lei, PhD): http://www.geneticsandhealth.com/2006/07/01/mendels-garden-2-the-best-of-genetics-blogging/#more-919
Genetics and Health: Archive for the 'Featured Genetics and Health Blogs' Category (By Hsien Hsien Lei, PhD): http://www.geneticsandhealth.com/category/genetics-blogging/featured-blogs/
Google: Blog Search: inblogtitle:"(omics OR genomics OR proteomics OR bioinformatics OR nanotechnology)"
* SEARCHING FOR BLOG ENTRIES ON A TOPIC
Feedster: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)
Google Blog Search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)
IceRocket: Blog Search Engine: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)
Technorati: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)
More blog search engines:
Anderson, PF. "Tasks: Blogs, Blog Search & RSS Feeds." The Eight-fold Path to Right Searching: Tips, Tasks, & Tools. http://www-personal.umich.edu/~pfa/pro/8fold/taskblogs.html
Posted by pfa at 04:42 PM | Comments (0)
August 15, 2006
New Articles from UM SoD Faculty: August 06, part 1
Chun YH. Yamakoshi Y. Kim JW. Iwata T. Hu JC. Simmer JP.
Porcine SPARC: isolation from dentin, cDNA sequence, and computer model.
European Journal of Oral Sciences. 114 Suppl 1:78-85; discussion 93-5, 379-80, 2006 May.
PMID: 16674666
Kim JW. Simmer JP. Lin BP. Seymen F. Bartlett JD. Hu JC.
Mutational analysis of candidate genes in 24 amelogenesis imperfecta families.
European Journal of Oral Sciences. 114 Suppl 1:3-12; discussion 39-41, 379, 2006 May.
PMID: 16674655
Lorenzi PL. Landowski CP. Brancale A. Song X. Townsend LB. Drach JC. Amidon GL.
N-methylpurine DNA glycosylase and 8-oxoguanine dna glycosylase metabolize the antiviral nucleoside 2-bromo-5,6-dichloro-1-(beta-D-ribofuranosyl)benzimidazole.
Drug Metabolism & Disposition. 34(6):1070-7, 2006 Jun.
PMID: 16565170
Nriagu J. Burt B. Linder A. Ismail A. Sohn W.
Lead levels in blood and saliva in a low-income population of Detroit, Michigan.
International Journal of Hygiene & Environmental Health. 209(2):109-21, 2006 Mar.
PMID: 16443391
Phimphilai M. Zhao Z. Boules H. Roca H. Franceschi RT.
BMP signaling is required for RUNX2-dependent induction of the osteoblast phenotype.
Journal of Bone & Mineral Research. 21(4):637-46, 2006 Apr.
PMID: 16598384
Terashi H. Izumi K. Deveci M. Rhodes LM. Marcelo CL.
High glucose inhibits human epidermal keratinocyte proliferation for cellular studies on diabetes mellitus.
International Wound Journal. 2(4):298-304, 2005 Dec.
PMID: 16618316
Yamakoshi Y. Hu JC. Fukae M. Yamakoshi F. Simmer JP.
How do enamelysin and kallikrein 4 process the 32-kDa enamelin?.
European Journal of Oral Sciences. 114 Suppl 1:45-51; discussion 93-5, 379-80, 2006 May.
PMID: 16674662
Yamakoshi Y. Hu JC. Zhang H. Iwata T. Yamakoshi F. Simmer JP.
Proteomic analysis of enamel matrix using a two-dimensional protein fractionation system.
European Journal of Oral Sciences. 114 Suppl 1:266-71; discussion 285-6, 382, 2006 May.
PMID: 16674696
Posted by pfa at 02:33 PM | Comments (0)
News Flash: Nicotine ... Protects?
The Parkinson's Institute: Nicotine Found to Protect Against Parkinson's-Like Brain Damage:
http://www.thepi.org/altruesite/files/parkinson/News/TPI%20Nicotine%20Research%20Press%20Release.html
Chronic oral nicotine treatment protects against striatal degeneration in MPTP-treated primates / Journal of Neurochemistry: (Online Early: Published article online 01 Aug 2006)
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-4159.2006.04078.x
Posted by pfa at 02:25 PM | Comments (0)
August 09, 2006
Omics Wikis & Community Tools (Omics Series, 22)
For many decades, research on scientific information use has shown that researchers prefer to ask their friends and colleagues and prior teachers for information they need above and beyond all other sources. The Internet has always supported communal editing of documents, and as new tools are developed to support community information sharing and communal editing, it is now making it even easier for communities (scientific or not) to share information, questions, and the process of discovery. A prime example of this is the question of human survival recently posed by Stephen Hawking to Yahoo Answers, which garnered over 25,000 responses from a diverse online community.
Links About Stephen Hawking's Question: http://del.icio.us/dentlib/hawking.stephen
In today's blog entry, we will explore some of the tools being used by scientists and researchers to share research resources (including citations) and create common information tools.
* FOLKSONOMY & COMMUNITY TOOLS
Folksonomy tools are the kind described above, allowing a community of people with shared interests to share resources, citations, and information they have found, and to comment on what they or others have discovered. Three of the most popular folksonomy tools for researchers include Connotea, CiteULike and Del.icio.us.
Connotea (Nature): http://www.connotea.org/
CiteULike: http://www.citeulike.org/
Del.icio.us: http://del.icio.us/
Each of these free resources allows individuals to create their own account and track or capture information they've found, keeping the links or information handy online. This means it is accessible from home, work, school, conferences, or other places, as long as you have an Internet connection and a web browser. Connotea and CiteULike are both intended primarily for capturing citations / articles. Del.icio.us is primarily used for capturing bookmarks / webpages. With Del.icio.us you can import and export bookmarks from any computer you use, allowing you to create a master set of bookmarks available on any computer you use.
With all of these systems, people usually add descriptive comments and/or "tags". Tags are subject terms that you choose to describe the item. You can then click on a tag and see every item that shares the same tag. Some individuals have become rather well-known for their collections of resources on a specific topic. Vannevar Bush would have called these people "trailblazers." Here are two exmples of persons respected for their omics collections.
Del.icio.us: RPiquepa: Nanotechnology: http://del.icio.us/rpiquepa/Nanotechnology
CiteULike: TimyU: Genomics: http://www.citeulike.org/user/timyu/tag/genomics
Another great way to explore collections without having to know who is collecting is simply to browse by tag. All three of today's tools use similar formats for the URLs for browsing by tag (a.k.a. subject heading). You can guess what might be a tag, and then see if anyone else is using it, and what they have discovered. Items are usually displayed with the most recently added items on top, and older items toward the far end of the list. You can use these examples of URLs for browse-by-tag, and edit the end of the web address for the term you want to use. Usually capitalization doesn't make a difference, but you may want to try a word both ways just to be sure.
CiteULike: Tag: Bioinformatics: http://www.citeulike.org/tag/bioinformatics
Connotea (Nature): Tag; Proteomics: http://www.connotea.org/tag/proteomics
Del.icio.us: Tag: Genomics: http://del.icio.us/tag/genomics
When browsing by tag, if you noticed a person who seems to be collecting a lot of items or resources that interest you, you may want to browse that person's collection. You can usually do this by either clicking on the person's name or account. If accounts are not listed, you can sometimes discover who it is that collected an item by clicking on a text link that says something like "saved by 10 other people".
In any case, the various folksonomy tools can become a tool of inestimable value in staying current and discovering new resources and articles in your area of interest.
* WIKIS
The folksonomy tools like CiteULike, Connotea, and Del.icio.us all allow you personal control over your collections and information. Another approach are wikis, which are true communal efforts. In a wiki, for example Wikipedia, a community collectively edit information resources on a topic of shared interest. For Wikipedia, the community is very large, potentially open to the world. Many other wikis are less open, and may be restricted to members of an association, or to a particular research lab or other administrative unit, or however else a community defines itself. Some wikis are viewable by the world, but can only be edited by the "insiders" for that community, while others restrict both viewing and editing. Here are some examples of wikis available to persons interested in omics.
Bio-Pedia, an openfree bioinformation encyclopedia: http://biocc.ngic.re.kr/Biopedia/Biowiki/index.php/Main_Page
BioWiki: http://biowiki.org/BioWikis
BiWiki: Bingen Bioinformatics Wiki: http://biwiki.fh-bingen.de/biwiki
Evolving Code Wiki: http://www.evolvingcode.net/index.php
Fred Hutchinson Computational Proteomics Laboratory (CPL) Proteomics Repository: https://proteomics.fhcrc.org/CPAS/Project/home/home.view
GUS: The Genomics Unified Schema: http://www.gusdb.org/wiki
Molecular Station: Molecular Biology Encyclopedia: Molecular Wiki: http://wiki.molecularstation.com/
nodalpoint [nodalpoint wiki] (bioinformatics): http://wiki.nodalpoint.org/
Omics Wiki: http://biocc.ngic.re.kr/Omics/Mediawiki/index.php/Main_Page
Open Bioinformatics Foundation (OBF): http://www.open-bio.org/wiki/Main_Page
Proteomics Wiki (subscription required) [German/English]: http://elbanet.ethz.ch/wikifarm/proteomics/
Wesleyan's Genomics Wiki Web: http://twiki.wesleyan.edu/cgi-bin/view/Genomics/WebHome
Wikiomics Bioinformatics Wiki: http://wikiomics.org
Wise-Nano Project: http://wise-nano.org/w/Main_Page
Posted by pfa at 10:59 AM | Comments (0)
August 07, 2006
Staying Current: Omics Press & News Sources (Omics Series, 21)
Staying current with new developments is partly a matter of keeping abreast of the research journals (as discussed in an earlier entry), but also see what is in the recent press, nationally and globally. You can do this by looking for news from major newswire services, from the web news portals, or by going to science or omics news portals. This entry is organized from specific to general, beginning with omics and nano news sources, followed by regional science news, general science news portals, and ideas for how to find omics news in generic news portals included in our "Want More?" section.
* OMICS NEWS PORTALS & SERVICES
Bioinfo Online: http://www.bioinfo-online.net/
GeneLetter: Genetics News: http://www.geneletter.com/index.epl
Genome News Network (GNN): http://www.genomenewsnetwork.org/
GenomicsProteomics: http://www.genomicsproteomics.com
Metabolomics: http://www.metabolomics.net
Nature Omics Gateway: http://www.nature.com/omics/
ProteinCrystallography: http://www.proteincrystallography.com
Proteomics NEWS @CPRMap - Clinical Proteomics Research Map: http://www.cprmap.com/proteomics-news/
RNAi.net: http://www.RNAi.net
ScienceGenomics.org (Science Functional Genomics): News: http://www.sciencemag.org/feature/plus/sfg/
Syndicated Bioinformatics News and Biotechnology News: http://news.biohealthmatics.com/
* NANOTECHNOLOGY NEWS PORTALS & SERVICES
Nanodot: Nanotechnology News and Discussion: http://www.foresight.org/nanodot/
NanoTechnology: http://www.NanoTechnology.net
Nanotechnology.com: http://www.nanotechnology.com/
Nanotechnology News - Current Month's News: http://www.nanotech-now.com/current-months-news.htm
Nanotechnology News Network: http://www.nanonewsnet.com/
Nature: Materials science and nanotechnology: http://www.nature.com/materials/
Scientific American: Nanotechnology: http://www.sciam.com/nanotech/
Small Times: News about MEMS, Nanotechnology and Microsystems: http://www.smalltimes.com/
Yahoo! News: Nanotechnology Full Coverage: http://news.yahoo.com/fc/Tech/Nanotechnology
* REGIONAL SCIENCE NEWS
EurActiv.com: Science: http://www.euractiv.com/en/science
European Commission: Research: Fundamental Genomics: Newsletters: http://ec.europa.eu/research/health/genomics/newsletter/newsletters_en.htm
European Commission: CORDIS Express, weekly briefing on European Research and Innovation from CORDIS (Community Research and Development Information Service): http://ec.europa.eu/research/cordis-express_en.cfm
National Science Foundation (NSF): News: http://nsf.gov/news/
CBC.ca: Health & Science News: http://www.cbc.ca/science/
SciDev.net, Science and Development Network: http://www.scidev.net/
* SCIENCE NEWS PORTALS
AAAS: Eurekalert: http://www.eurekalert.org/
BrightSurf: Today's Science News and Current Science Events: http://brightsurf.com/
INCLUDES:
- Bioinformatics News
- Genomics News
- Nanotechnology News
- Omics News
- Proteomics News
- Transgenic News
FirstScience.com: http://www.firstscience.com/
NewScientist: http://www.newscientist.com/
SciCentral: http://www.scicentral.com/
ScienceDaily: http://www.sciencedaily.com/
Science News and Genomics: A Global Resource: http://science.bio.org/
Science News Online: http://www.sciencenews.org/
* WANT MORE?
Remember, you can add words to these searches to focus on an area of interest.
Google News search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified")
Yahoo News search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified")
Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified") (news OR "press release")
Rollyo: pfa: Science News Search: http://rollyo.com/pfa/science_news/
Rollyo: robert1066: Technology & Science News Search: http://www.rollyo.com/robert1066/technology_science_news/
Posted by pfa at 04:40 PM | Comments (0)
August 05, 2006
Historical Photos: Dental Promotion Campaigns
Case Western Reserve University: Dittrick Medical History Center: Photography of Dental Care Campaigns 1909 -1919: http://www.case.edu/artsci/dittrick/site2/pics/dental.htm
This marvelous little online exhibit begins with a few photos, but continues with stories about how dentistry used to be. No horror stories, just the origins of dental hygiene, what a dental exam was like before x-rays, and other interesting tidbits from Cleveland in the early 1900s.
Posted by pfa at 07:46 AM | Comments (0)
August 04, 2006
Staying Current: Omics Journals Online (Omics Series, 20)
The omics fields have become real leaders in the idea of open access. Researchers in these cutting edge fields have found that rapid ready access to the newest research benefits them all. There is a perhaps surprising number of journals providing high quality research either completely freely online or following various models. A publication model found in omics journals that is less common among other disciplines, in my personal experience, is that of having free access for 30 days, after which access is restricted to subscribers.
Today's blog entry includes a selection of omics journals available free online, followed by selections of electronic journals available to the University of Michigan community. Last but not least, we include a structured web search for those who would like to see some of the journals we did not include today.
* OPEN ACCCESS JOURNALS
AZojono - Journal of Nanotechnology Online: http://www.azonano.com/nanotechnology.asp
BioInform (bio1nf0rm): http://www.bioinform.com/issues/
Bioinformation: http://www.bioinformation.net/
Biomarker Insights: http://www.la-press.com/bmi.htm
BMC genomics: http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=32
Comparative and Functional Genomics: http://www.hindawi.com/GetJournal.aspx?journal=CFG
EURASIP Journal on Bioinformatics and Systems Biology: http://www.hindawi.com/journals/bsb/
Genetic Engineering News: http://www.genengnews.com/
This title has an Omics skills-building tutorial article in almost every issue of the journal.
GenomeBiology.com: http://genomebiology.com/ OR http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=7
Genome informatics online (Workshop on Genome Informatics): http://www.jsbi.org/journal.html
Genome research (Cold Spring Harbor Laboratory Press): http://www.genome.org/ ($$)
Genomics and Health Weekly Update (CDC: National Office of Public Health Genomics): http://www.cdc.gov/genomics/update/current.htm
Genomics & proteomics (G&P): http://www.genpromag.com/
Genomics, Society and Policy Online Journal:http://www.gspjournal.com/
Human Genome News (National Institutes of Health: National Center for Human Genome Research): http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/hgn.shtml
Internet Electronic Journal of Molecular Design: http://www.biochempress.com/
Internet Journal of Genomics and Proteomics: http://www.ispub.com/ostia/index.php?xmlFilePath=journals/ijgp/front.xml
Molecular & cellular proteomics : MCP: http://www.mcponline.org/
Nanoscale Research Letters: http://www.springer.com/east/home/generic/search/results?SGWID=5-40109-70-173663905-0
"Nanoscale Research Letters (NRL) is the first nanotechnology journal from a major commercial publisher to publish articles with open access."
Nanotechnology: http://www.iop.org/EJ/journal/Nano
"As a service to authors, all papers published in our journals are free for 30 days from the date of online publication."
Physiological genomics: http://physiolgenomics.physiology.org/
PLoS Computational Biology: http://compbiol.plosjournals.org/perlserv/?request=index-html&issn=1553-7358
* UM ACCESS VIA MIRLYN OR SEARCHTOOLS:
This is just a small sampling of the additional electronic journals and journal archives available as a member of the University of Michigan community. These can be accessed via either Mirlyn or SearchTools. You can also browse electronic journals at the University Library Electronic Journals & Newspapers List. There are also many print journals available on the various omics topics in campus libraries.
Annual review of genomics and human genetics.
Briefings in functional genomics & proteomics
Comparative and functional genomics
Cytogenetic and genome research.
Functional & integrative genomics.
Genomics.
Human genome abstracts
IEEE transactions on nanotechnology.
Journal of biomedical nanotechnology.
Journal of structural and functional genomics
Mammalian genome : official journal of the International Mammalian Genome Society.
Microbial & comparative genomics
Molecular genetics and genomics : MGG.
Nano- and microtechnology : materials, processes, packaging and systems (SPIE--the International Society for Optical Engineering)
Nanobiotechnology : the journal at the intersection of nanotechnology, molecular biology, and biomedical sciences.
Nano letters (American Chemical Society)
Nanotechnology (SPIE--the International Society for Optical Engineering).
Omics
Pharmacogenetics and genomics.
Proteomics.
Smart structures and materials. Smart electronics, MEMS, and nanotechnology.
* WANT MORE?
Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (journal OR subscribe OR subscription OR "open access")
Posted by pfa at 02:34 PM | Comments (0)
New ADA Site on the Future of Dental Education
Dental Education - Our Legacy, Our Future
http://www.ourlegacyourfuture.org/
"A strong dental education system is vital to the future of the dental profession and the future of the public's oral health. Dental education is the foundation from which all dentistry is built and sustained. The knowledge, science, critical-thinking skills and ethical principles needed to become a dentist are first developed in dental school.
Dental Education: Our Legacy - Our Future is a collaborative effort by various partner organizations to raise awareness of the challenges facing dental education in the U.S. and to promote a culture of philanthropy within dentistry to address these issues."
Posted by pfa at 02:31 PM | Comments (0)
August 03, 2006
Finding Omics Grants and Funding Opportunities (Omics Series, 19)
Funding is core to making it possible to have innovative and cutting edge research in the omics areas. There are a variety of resources generally available for researchers to discover grants and funding opportunities. Most UM researchers are intimately aware of the UM Research web site and what it has to offer. Please also take a look at the University Library guide on foundation and grant resources. There are in addition a number of special organizations that gather or provide grants specifically for these research areas.
* CAMPUS RESOURCES
UM Research: http://www.research.umich.edu/
INCLUDES:
Funding Opportunities: http://www.research.umich.edu/funding/funding.html
Grants.gov & the University of Michigan: http://www.research.umich.edu/era/grantsgov/index.html
Research Administrator Toolkit: http://www.research.umich.edu/ralinks/
University Library: Government Publications: Federal Government Resources on the Web/Grants and Contracts: http://www.lib.umich.edu/govdocs/fedgt.html
University Library: Government Publications: Michigan/Grants and Auctions: http://www.lib.umich.edu/govdocs/michgrt.html
University Library: Graduate Library Subject Guides: Resources on Foundations and Grants: http://www.lib.umich.edu/grad/guide/guide.php?id=84
* NATIONAL
Cancer.gov: NCI Alliance for Nanotechnology in Cancer: Funding Opportunities: http://nano.cancer.gov/resource_center/funding.asp
CDC: National Office of Public Health Genomics: Genomic Funding: http://www.cdc.gov/genomics/activities/funding.htm
genome.gov: Grants: http://www.genome.gov/10000004
National Center for Research Resources: Research Funding Opportunities: http://www.ncrr.nih.gov/rsrch_funding.asp
National Institutes of Health: Biomedical Information Science and Technology Initiative (BISTI): Bioinformatics Funding Opportunities Page: http://www.bisti.nih.gov/bistic_funding.cfm
National Institutes of Health: National Institute of Dental and Craniofacial Research: http://www.nidcr.nih.gov/Funding/CurrentFundingOpportunities/default.htm
National Nanotechnology Initiative: Funding Opportunities: http://www.nano.gov/html/funding/home_funding.html
National Science Foundation: Find Funding: http://www.nsf.gov/funding/
* INTERNATIONAL
Biotechnology and Biological Sciences Research Council (BBSRC): How to get Funding: http://www.bbsrc.ac.uk/funding/Welcome.html
Nanoforum: Funding and Support for International Nanotechnology Collaborations: http://www.nanoforum.org/nf06~modul~showmore~folder~99999~scid~351~.html?action=longview_publication&
World Health Organization (WHO): Grant Opportunites: http://www.who.int/tdr/grants/default.htm
* WANT MORE?
Posted by pfa at 11:47 AM | Comments (0)
August 02, 2006
Omics Standards (Omics Series, 18)
As with most new fields, as the discipline reaches maturity there is a call for standards and guidelines, both relating to practice as well as to terminology. The omics fields have reached that maturity with astonishing rapidity, and have had standards development efforts underway for a few years now. In thte resources listed below, you will find standards organizations at international, national, and topical levels; background information about standardization efforts in the omics fields; and much more. For University of Michigan patrons, we would like to highlight the marvelous resource from the Art, Architecture and Engineering Library on the many standards resources available to our campus. Again, we close the blog entry with a web search for those interested in finding more on this topic.
* STANDARDS, SPECIFICATIONS & GUIDELINES
Foresight Institute: Molecular Nanotechnology Guidelines: http://www.foresight.org/guidelines/
* COLLECTIONS, GUIDES AND SOURCES:
University Library: Art, Architecture and Engineering Library: Standards: http://www.lib.umich.edu/aael/division.php?divisionID=16&d=v
Georgia Tech Library: Nanoscience & Nanotechnology: Standards & Specifications: http://www.library.gatech.edu/research_help/subject/index.php?/nanoscience/standards
National Institute of Standards and Technology (NIST): Research by Subject: Nanotechnology: http://nvl.nist.gov/nvl2.cfm?dynamic=res_subj&subjectid=17
IEEE Standards Online: Nanotechnology Standards: http://standards.ieee.org/catalog/olis/nanotech.html [Requires UM login, access via AAEL page]
* STANDARDS ORGANIZATIONS:
American National Standards Institute's Nanotechnology Standards Panel (ANSI-NSP): http://www.ansi.org/standards_activities/standards_boards_panels/nsp/overview.aspx?menuid=3
Association of Biomolecular Resource Facilities (ABRF): Proteomics Standards Research Group Research Group: http://www.abrf.org/index.cfm/group.show/ProteomicsStandardsResearchGroup.47.htm
HUPO (HUman Proteome Organization): Proteomics Standards Initiative: http://psidev.sourceforge.net/
"The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification."
ISO - International Organization for Standardization: TC229, Nanotechnologies: http://www.iso.org/iso/en/stdsdevelopment/tc/tclist/TechnicalCommitteeDetailPage.TechnicalCommitteeDetail?COMMID=5932
Microarray Gene Expression Data Society: http://www.mged.org/
SOFG (Standards and Ontologies for Functional Genomics): http://www.sofg.org/
* ABOUT OMICS STANDARDIZATION EFFORTS:
Capello, Jolinda. Overview of Nanotechnology: Risks, Initiatives and Standardization. American Society of Safety Engineers: http://www.asse.org/nantechArticle.htm
European Bioinformatics Institute: Meetings: Proteomics Standards Initiative: http://www.ebi.ac.uk/Information/meetings/psi.html
European Science Foundation: Integrated Approaches for Functional Genomics: Standardisation, benchmarking and comparision of different experimental systems: http://www.functionalgenomics.org.uk/sections/programme/standardisation.htm
IEEE Standards Association: Nanotechnology Standards Initiatives at IEEE: http://standards.ieee.org/announcements/bkgnd_nanostdsinit.html
National Institute of Standards and Technology: Nanotechnology Is BIG at NIST: http://www.nist.gov/nanotech/
NIH Roadmap: Standards in Proteomics Workshop: Agenda: http://nihroadmap.nih.gov/buildingblocks/proteomics/
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Posted by pfa at 09:41 PM | Comments (0)
August 01, 2006
Other Databases for Omics Researchers (Omics Series, 17)
The premiere source of omics databases is of course the collection available from NIH-NLM-NCBI (Blast, OMIM, etc). These were highlighted in a previous blog entry in this series (#9). For the current blog entry, we have selected examples of omics databases made available from various research centers, institutes and organizations around the world. We included only collections of databases, or specific databases that were free and openly available at the time of writing. There are many more that require subscription. As you can see, there are also many that do not.
* OMICS DATABASE COLLECTIONS
Kyoto University Bioinformatics Center: Genome Databases in Japan: http://www.genome.jp/genome_db/
NIH: Computational Molecular Biology: Databases: http://molbio.info.nih.gov/molbio/db.html
Proteomic World: Databases: http://www.proteomicworld.org/DatabasePage.html
* DATABASES FROM SPECIFIC PROJECTS
Baylor College of Medicine: Department of Pharmacology: Small RNA database: http://condor.bcm.tmc.edu/smallRNA/smallrna.html
BioGRID: A General Repository for Interaction Datasets: http://www.thebiogrid.org/
Bioinformatics.org, Open-Source Bioinformatics for Researchers: Online Databases: http://bioinformatics.org/
- Online Databases EST Clusters: http://bioinformatics.org/zest/
- Immigrant Genes: http://bioinformatics.org/immigrant/
- Leukemia Genes: http://bioinformatics.org/legend/
- p53 Tumor Protein Gene: http://bioinformatics.org/p53/
- Pancreatic Cancer Genes: http://bioinformatics.org/pcgdb/
- TB Drug Targets: http://bioinformatics.org/tbdtdb/
- T2K Acronym Finder: http://bioinformatics.org/textknowledge/
European Bioinformatics Institute (EMBL-EBI): IntAct Interaction Database: http://www.ebi.ac.uk/intact/index.jsp
"IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available."
European Bioinformatics Institute (EMBL-EBI): PRIDE (PRoteomics IDEntifications database): http://www.ebi.ac.uk/pride/
Georgetown University Medical Center: Protein Information Resource (Integrated Protein Informatics Resource for Genomic and Proteomic Research): http://pir.georgetown.edu/pirwww/index.shtml
Georgetown University Medical Center: Protein Information Resource: Search & Analysis Tools: http://pir.georgetown.edu/pirwww/search/
Harvard University: Dana Farber Cancer Institute: WorfDB, The C. elegans ORFeome cloning project: http://worfdb.dfci.harvard.edu/
Harvard University: Harvard Institute of Proteomics: FlexGene Database: http://kotel.harvard.edu:8080/FLEX/welcome.jsp
Kyoto University Bioinformatics Center: DBGET: Web of Molecular Biology Databases: http://www.genome.jp/dbget/
MedicalComputing.net: Search Human Gene Information Database: http://www.medicalcomputing.net/cgi-bin/query_human_gene_info
MHCPEP [A database of MHC binding peptides (v. 1.3)]: http://wehih.wehi.edu.au/mhcpep/
Entries include: " ... the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references."
NanoWerk: NanoBank: Nanomaterials Database: http://www.nanowerk.com/phpscripts/n_dbsearch.php
Real Time Primers, validated primer sets for quantitative real time PCR: http://www.realtimeprimers.org/
RNA Interference, database of siRNA sequences and RNA inhibition studies: http://www.rnainterference.org/
Rutgers State University of New Jersey: The Nucleic Acid Database Project:
Nucleic Acid Database (NDB): http://ndbserver.rutgers.edu/
University of Texas: Bioinformatics, Proteomics, and Functional Genomics: Open Proteomics Database: http://apropos.icmb.utexas.edu/OPD/
"OPD is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 3,000,000 spectra representing experiments from 5 different organisms."
Weizmann Institute of Science: GeneCards: http://www.genecards.org/index.shtml
"GeneCards is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies."
World Health Organization (WHO): International Database on Craniofacial Anomalies (IDCFA): http://www.who.int/genomics/anomalies/idcfa/en/
WormBase: http://www.wormbase.org/
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Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (database OR dataset OR search)
Posted by pfa at 04:42 PM | Comments (0)