tag:blogger.com,1999:blog-10839418411325832952024-03-08T10:02:38.969-07:00Bio5 librariansResources for the University of Arizona Bio5 and Medical Research Groups.Unknownnoreply@blogger.comBlogger29125tag:blogger.com,1999:blog-1083941841132583295.post-9353053878401955462008-09-11T15:30:00.000-07:002008-09-11T15:32:37.520-07:00WikipediaWikipedia covers a wide range of genomic, biologic and engineering topics, many in detail and with reasonable exprtise. <br /><ul><li><a href="http://en.wikipedia.org/wiki/Genomics">Genomoic</a></li><li><a href="http://en.wikipedia.org/wiki/Engineering">Engineering</a></li></ul>Unknownnoreply@blogger.com2tag:blogger.com,1999:blog-1083941841132583295.post-71216097279581491082007-08-24T10:56:00.001-07:002008-09-11T15:41:43.295-07:00SciVee<a style="font-weight: bold;" href="http://www.scivee.tv/">SciVee</a> provides a place for scientists to upload a short video about a recent article -- the equivalent of a conference presentation. In its current beta version, only articles published in PLOS can be SciVee'd, but the next version will accept any article in <a href="http://www.pubmedcentral.nih.gov/">PubMed Central</a>. The majority of journal publishers put articles in PubMed Central 6-18 months after publication.<br /><br />SciVee is a joint effort of the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC.)Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-68614935779910218072007-08-20T12:26:00.000-07:002007-08-20T12:28:36.410-07:00Bio5/MRB InfoSources Series, Fall 2007<span style="font-weight: bold;">Wednesdays - August 29 - September 26, 2007</span><br /><span style="font-weight: bold;">Noon in Keating, Room 103</span><br /><span style="font-weight: bold;">Free lunch provided</span><br /><br /><span style="font-weight: bold;">Aug 29</span> What impact are you making (and where can you get funding for it?)<br />Two brief presentations on:<br />- Journal Impact Factors via the JCR database, and open access journals.<br />- Search grant sources such as Community of Science and CRISP.<br /><br /><span style="font-weight: bold;">Sept 5</span> UA InfoSources - the key to research success<br />A speedy tour of ebooks, ejournals, databases, interlibrary loan and other services available to Bio5 researchers.<br /><br /><span style="font-weight: bold;">Sept 12</span> The Business of Science<br />BioScan and other Business Databases - How to locate information about U.S. and foreign companies actively involved in biotech research and development.<br /><br /><span style="font-weight: bold;">Sept 19</span> SciFinder Scholar 2007<br />An overview of the latest interface to Chemical Abstracts Online, providing highly customizable searching.<br /><br /><span style="font-weight: bold;">Sept 26 </span>RefWorks & Web of Science<br />A Find it > Save it > Cite it workshop. Two brief presentations on:<br />- Using Web of Science to track the impact of your research and follow a topic both forwards and backwards in time<br />- Learn how to gather and organize your article and book citations for a variety of projects online using RefWorks.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-72417340122508050702007-08-02T09:35:00.000-07:002007-08-02T10:04:31.662-07:00NC3Rs - Mouse databases<a href="http://www.nc3rs.org.uk/category.asp?catID=8">NC3Rs - Mouse databases</a> is an extremely throrough and up-to-date guide to mouse information -- genomic, proteomic and strains. This NC3Rs guide describes online resources under these headings:<br /><ul> <li>Conditional mouse models databases - 2 resources<br /> </li> <li>Transgenic and knockout databases - 3 resources</li> <li>Mouse strain repositories - 4 resources</li> <li>Mouse pathology - 2 resources</li> <li>Mouse genetics and genomics - 8 resources</li> <li>Comprehensive mouse links - 4 resources</li> </ul> The sidebar links to more interactive resources, such as working group white papers and listservs.Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1083941841132583295.post-3725736256378679792007-07-30T08:17:00.000-07:002007-08-01T14:58:04.845-07:00Medicago truncatula -- MedicCycA recent article from Bioinformatics discusses a visual biochemical pathway database -- <a href="http://www.noble.org/MedicCyc/">MedicCyc</a> -- for <span style="font-style: italic;">Medicago truncatula</span> -- "Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites."<br /><blockquote>Urbanczyk-Wochniak E, Sumner LW. MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 2007 Jun 1;23(11):1418-23. Epub 2007 Mar 7.</blockquote><a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/23/11/1418">Article</a><br /><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17344243&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">PubMed</a>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1083941841132583295.post-69734841641156599942007-07-24T16:30:00.000-07:002007-07-25T11:09:56.413-07:00Illumina BeadChip platform<span style="font-weight: bold;">Illumina Seminar<br /> Keating Room 103 -- Large Meeting room off of Lobby</span><br />GATC will be hosting a seminar from Illumina concerning the applications of their "next generation sequencing"platform. The topics being presented are:<br /><ul> <li>Whole Genome and Candidate Resequencing</li> <li>SNP Mutation Discovery</li> <li>Digital Gene Expression Profiling</li> <li>ChIP by Sequence Tagging</li> <li>Small RNA/miRNA Identification and Quantitation</li> </ul> All are welcome to attend, the talk should last about an hour and there will be<br /> time for questions after. Call or email Ryan Sprissler / 520.621.9184 / ryans1@email.arizona.edu<br /><br />---<br />A <span style="font-weight: bold;">recent article</span> describes <span style="font-weight: bold;">IlluminaGUI</span> -- a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform <span style="text-decoration: underline;"><br /><br /></span>Article -- <a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/23/11/1431">IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform</a><br /><br /><a style="font-weight: bold;" href="http://illuminagui.dnsalias.org/">Link</a>Unknownnoreply@blogger.com2tag:blogger.com,1999:blog-1083941841132583295.post-35587077410013017182007-07-16T08:57:00.000-07:002007-07-16T09:30:45.675-07:00CRISPRdb database<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp0.blogger.com/_DyTQVqf4aI8/RpubC32MaOI/AAAAAAAAABc/B-vn2qbOqpI/s1600-h/crispr.gif"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://bp0.blogger.com/_DyTQVqf4aI8/RpubC32MaOI/AAAAAAAAABc/B-vn2qbOqpI/s400/crispr.gif" alt="CRISPR Browse" id="BLOGGER_PHOTO_ID_5087830677698406626" border="0" /></a><br /><br />The <span style="font-weight: bold;">CRISPRdb database</span> is a browsable sequence-database of "clustered regularly interspaced short palindromic repeats" from Archeae and Bacteria.<br /><br />Each month, the CRISPRFinder program searches several sources for new CRISPRs, and updates the CRISPRdb database. CRISPRFinder can be downloaded and used to search locally generated data as well.<br /><br /><br /><span style="font-weight: bold;"> - </span><a style="font-weight: bold;" href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17521438&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">About</a><br /><span style="font-weight: bold;"> - </span><a style="font-weight: bold;" href="http://crispr.u-psud.fr/crispr">Link</a><br /><br /><span style="font-weight: bold;">Browse by</span><br />- <a href="http://crispr.u-psud.fr/crispr/CRISPRdatabase.php?page=tax">View the strains taxonomy browser</a><br />- <a href="http://crispr.u-psud.fr/crispr/CRISPRdatabase.php?page=list">View the strains alphabetical browser</a><br />- <a href="http://crispr.u-psud.fr/crispr/CRISPRdatabase.php?page=process">View the strains in database processing order</a><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp0.blogger.com/_DyTQVqf4aI8/RpubC32MaPI/AAAAAAAAABk/X29aXo_D39w/s1600-h/cripr2.gif"><br /></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-88179752961681624422007-07-06T12:29:00.000-07:002007-07-06T12:53:12.960-07:00Allen Brain AtlasThe <a href="http://www.brainatlas.org/aba/">Neuroscience Gateway</a>, published in association with Nature, focuses on the <span style="font-style: italic;">genetics</span> of the mammalian brain. Its <a href="http://www.brain-map.org/"><span style="font-weight: bold;">Allen Brain Atlas</span></a> can be searched by gene names, markers and symbols, anatomic structure or fine structure annotation. It can be browsed by<br /><ul> <li>Structure -- <span style="font-size:78%;">Cerebellum / Cerebral cortex / Hippocampal region / Hippocampal formation / Hypothalamus / Lateral septal complex / Midbrain / Medulla / Olfactory bulb / Pons / Pallidum / Retrohippocampal region / Striatum-like amygdalar nuclei / Striatum / Striatum dorsal region / Striatum ventral region / Thalamus </span></li> <li>Gene symbol </li> <li>Images -- <span style="font-size:78%;">Coronal or Sagittal</span></li> </ul> Searches return basic information about the gene, plus links to NCBI and other sources. Running your mouse over the Epression Level/Expression Density bar changes the image to show the anatomic area.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp2.blogger.com/_DyTQVqf4aI8/Ro6c5xvLMsI/AAAAAAAAABU/Es5G509fDiA/s1600-h/allen1.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://bp2.blogger.com/_DyTQVqf4aI8/Ro6c5xvLMsI/AAAAAAAAABU/Es5G509fDiA/s400/allen1.jpg" alt="" id="BLOGGER_PHOTO_ID_5084173545765548738" border="0" /></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-58735568231104248282007-07-02T11:39:00.000-07:002007-07-02T12:11:04.334-07:00Plant genomic/proteomic sources<span style="font-weight: bold;">PlantGDB</span> -- Plant Genome Database. "an NSF-funded project ... to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities."<br />- <a href="http://scholar.google.com/scholar?num=100&hl=en&lr=&cluster=16396367697830692134">About</a><br />- <a href="http://www.plantgdb.org/sitemap/search.php">Link</a><br /><a href="http://www.maizemap.org/"></a><br /><span style="font-weight: bold;">MIPS Plants Databases</span> - Munich Center for Protein Sequences set of databases "focuses on the bioinformatics of plant genomes. It developed from the Arabidopsis genome annotation group." Databases include maize, Arabidosis, rice, tomatoes, lotus, and Medicago. Notable for manual annotations.<br />- <a href="http://nar.oxfordjournals.org/cgi/content/abstract/27/1/44">About</a><br />- <a href="http://mips.gsf.de/proj/plant/jsf/index.jsp">Link</a><br /><a href="http://grain.jouy.inra.fr/gendatabasemirror.html"></a><br /><span style="font-weight: bold;">iMap</span> -- "Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs."<br />- <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=14594716">About</a><br />- <a href="http://www.maizemap.org/">Link</a><br /><br /><span style="font-weight: bold;">Other databases</span> -- "<a href="http://cse.nias.affrc.go.jp/shignak/chromosome.net/databases.html">DataBases: Web sites for Chromosome Researchers</a>." Scroll down to Plants.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-37928798823397364742007-06-29T13:31:00.000-07:002007-07-02T12:12:36.779-07:00Seminar - July 12, 11-1:00You are invited to a SPECIAL SEMINAR about “Novel Technology in Biosensors”<br />July 12th, 2007<br />11:00 am-1:00 pm<br />Kiewit Auditorium, <a href="http://iiewww.ccit.arizona.edu//uamap/staticLarge/222.html">Arizona Cancer Center</a><br /><br />Octet Using Biolayer Interferometry for Affordable,<br />Rapid, Label-Free, Real Time Kinetics Analysis.<br /><br />Kathi Williams<br />West Coast Field<br />Application Scientist<br /><br />Lunch will be provided.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-87984713011380003042007-06-29T10:08:00.000-07:002007-06-29T10:37:49.704-07:00Science News SourcesA number of web sites focus on science news.<br /><br /><a href="http://www.eurekalert.org/">EurekAlert!</a> is one of the best, produced by AAAS. For Bio5, the agriculture, biology and medicine sections are worth following each day. Its primary source is press releases from science centers for governments, universities and journals.<br /><br /><a href="http://www.sciencedaily.com/">ScienceDaily</a> is a far more commercial venture, but it includes a breaking news section updated every 15 minutes. Its Health and Plants sections are most interest to us.<br /><br />Science news aggregators such as <a href="http://news.google.com/?topic=t">Google News</a>, <a href="http://news.yahoo.com/i/753;_ylt=A0WTUcuwQYVGTCgB.Ris0NUE">Yahoo News</a>, <a href="http://www.cnn.com/TECH/space/">CNN</a> and <a href="http://news.bbc.co.uk/2/hi/science/nature/default.stm">BBC</a> tend to offer stories about science news, instead of straight science links.<br /><br /><a href="http://dir.yahoo.com/Science/News_and_Media/">Yahoo</a> and <a href="http://www.google.com/Top/Science/News_and_Media/">Google</a> both have directory listings for science news sources, with subcatories.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-67137579554924247502007-06-25T14:18:00.000-07:002007-06-25T14:51:39.291-07:00Human Protein Atlas - imagesThe <a href="http://www.proteinatlas.org/">Human Protein Atlas</a> is a database of "high resolution images of immunohistochemically stained tissues and cell lines" for normal and cancerous human proteins. The database can be searched by chromosome-location or by keyword. Note that every character -- including spaces -- is searched. "FTCD" is not the same as "FTCD ". Searchable terms include gene name, antibody ID (either CAB001519 or 1519 works), and descriptor terms such as protein names. Click on the Antibody ID to view annotation data; click on the link-dots to view Ensembl/NCBI/RefSeq/Uniprot info.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp2.blogger.com/_DyTQVqf4aI8/RoA4qdnDVTI/AAAAAAAAABE/wdrre-MqPOk/s1600-h/HPU.gif"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://bp2.blogger.com/_DyTQVqf4aI8/RoA4qdnDVTI/AAAAAAAAABE/wdrre-MqPOk/s400/HPU.gif" alt="" id="BLOGGER_PHOTO_ID_5080122681828005170" border="0" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp3.blogger.com/_DyTQVqf4aI8/RoA4qtnDVUI/AAAAAAAAABM/evZIyOZn6S0/s1600-h/hup-img.gif"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://bp3.blogger.com/_DyTQVqf4aI8/RoA4qtnDVUI/AAAAAAAAABM/evZIyOZn6S0/s400/hup-img.gif" alt="" id="BLOGGER_PHOTO_ID_5080122686122972482" border="0" /></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-74863350948096477552007-06-22T14:10:00.000-07:002007-06-22T14:18:43.491-07:00MedGadget: Biomedical engineering blog<a href="http://www.medgadget.com/">MedGadget </a>covers both consumer and research biomedical gadgets. Postings cover topics such as nasal drug delivery units, museum openings, nanotube carriers and weekly news reports on the latest biomedical engineering feats.Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1083941841132583295.post-63077944497445871022007-06-21T11:44:00.000-07:002007-06-21T11:55:21.050-07:00Nature's BlogsThe journal <span style="font-style: italic;">Nature </span>supports fifteen <a href="http://www.nature.com/blogs/index.html">blogs</a>, ranging from chemistry to climate to methods to biology. <br /><br /><a href="http://blog-msb.embo.org/blog/">Seven Stones</a> -- "The <span class="journal-name">Molecular Systems Biology</span> blog on systems and synthetic biology" -- works in conjunction with Nature's <a href="http://www.nature.com/msb/index.html">Molecular Systems Biology</a> page and the <a href="http://www.embo.org/">European Molecular Biology Organization</a> (EMBO.) Seven Stones covers systems and synthetic biology, including technical, scientific and societal issues. Conference presentations are summarized and discussed, as well as the journal literature. <br /><br /><span style="font-style: italic;">Nature </span>blogs provides links to news, and work with Connotea as well as Precedings.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-3143437264488409912007-06-20T15:12:00.000-07:002007-06-20T15:19:10.010-07:00Nature Precedings launches"<a href="http://precedings.nature.com/">Nature Precedings</a> is a free online service that enables researchers to rapidly share, discuss, and cite their early findings." It is modelled on the Pre-Print services common in astronomy and physics. Like other Web 2 services, it makes use of user-generated tags as well as formal subjects to classify information.<br /><br />There is a discussion on the use of Blogs in research -- <a href="http://precedings.nature.com/documents/39/version/1">http://precedings.nature.com/documents/39/version/1</a><br /><br /><a href="http://info.nature.com/cgi-bin24/DM/y/eedg0WKxk30Jyg0BVUp0Eg" eudora="autourl"><br /></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-80665119472060893372007-06-15T10:43:00.000-07:002007-06-15T10:50:45.106-07:00Translational research at UAUA received a <a href="http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-06-002.html">Clinical and Translational Science Award</a> (CTSA) to explore state-wide focus on translational research -- moving data from the lab to the bedside. Two major groups have come out of this at UA & ASU: <a href="http://www.abor.asu.edu/1_the_regents/TRIF/brochures/2007/UA%20ACTREC%20FINAL.pdf">ACTREC</a> & <a href="http://www.abor.asu.edu/1_the_regents/TRIF/brochures/2007/UA%20ACTREC%20FINAL.pdf">Clinical Scholars Circle</a>.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-26479839263134984582007-06-12T10:15:00.000-07:002007-06-12T10:20:38.975-07:00Sandwalk blogSandwalk - <a href="http://sandwalk.blogspot.com/">http://sandwalk.blogspot.com/</a> - is another biomedical blog, this one dedicated to biochemistry. Moran's "Monday Molecules" series offers a molecular challenge to be rewarded with a free lunch. The Bio5 librarians might want to emulate this challenge for our Bio5 folks.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-20739563277567729562007-05-31T14:08:00.000-07:002007-05-31T14:50:35.081-07:00CutDB: a proteolytic event database<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp3.blogger.com/_DyTQVqf4aI8/Rl9BFYMtxwI/AAAAAAAAAA0/vS_ewHg9dP0/s1600-h/via.gif"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer;" src="http://bp3.blogger.com/_DyTQVqf4aI8/Rl9BFYMtxwI/AAAAAAAAAA0/vS_ewHg9dP0/s320/via.gif" alt="" id="BLOGGER_PHOTO_ID_5070843266093401858" border="0" /></a>The <a href="http://www.burnham.org/">Burnham Institute for Medical Research</a> offers several databases, including PMAP CutDB. CutDB is a database of proteases and their proteolytic events - including predicted events - from experiments and the literature, at <a href="http://cutdb.burnham.org/">http://cutdb.burnham.org</a> It can be searched by a wide range of field, listed to the right. Some entries link to extensive lists of events such as furin, while others have only one entry such as griselysin.<br /><ul> <li>Clicking on the name in <span style="font-weight: bold;">[Protease_definition] </span>may lead to an entry in the PMAP-Proteases database.<br /></li><li>Clicking on the <span style="font-weight: bold;">[Substrate definition] </span> leads to its NCBI Protein entry.</li><li>Clicking on <span style="font-weight: bold;">[Structure]</span> links may crash your web browser - it seems to be highly MSIE/default settings dependent.<br /> </li> <li>Clicking on <span style="font-weight: bold;">[Details] </span>leads to an entry with substrate/structure, cut-site, cell line and original citation.</li> </ul><br /><div style="text-align: left;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp2.blogger.com/_DyTQVqf4aI8/Rl89HIMtxuI/AAAAAAAAAAk/aMeeU1g_suE/s1600-h/funin-list.gif"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://bp2.blogger.com/_DyTQVqf4aI8/Rl89HIMtxuI/AAAAAAAAAAk/aMeeU1g_suE/s400/funin-list.gif" alt="" id="BLOGGER_PHOTO_ID_5070838898111661794" border="0" /></a></div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bp2.blogger.com/_DyTQVqf4aI8/Rl89HIMtxvI/AAAAAAAAAAs/bDR7L-gW40k/s1600-h/gris-list.gif"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://bp2.blogger.com/_DyTQVqf4aI8/Rl89HIMtxvI/AAAAAAAAAAs/bDR7L-gW40k/s400/gris-list.gif" alt="" id="BLOGGER_PHOTO_ID_5070838898111661810" border="0" /></a><br /><a href="http://cutdb.burnham.org/relation/show/16491"></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-41578436607751695162007-05-29T11:25:00.000-07:002007-06-21T11:42:14.261-07:00KEGG LIGAND<a style="font-weight: bold;" href="http://www.genome.ad.jp/dbget/ligand.html">KEGG LIGAND</a> is an alternative to the NCBI databases, covering the "molecular building blocks of life in the chemical space." Its interlinking is simpler and more up-front than NCBI's -- if not as complete. The Reaction database is easy to use. Compare diethylene glycol in <a href="http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=%22Diethylene%20glycol%22">NCBI</a> and <a href="http://www.genome.ad.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=ligand&keywords=Diethylene+glycol&mode=bfind">LIGAND.</a><br /><br /><span style="font-weight: bold;">Article</span><br />Susumu Gotoa Takaaki Nishioka, and Minoru Kanehisa.<br />LIGAND: chemical database of enzyme reactions<a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=102410">.<br />Nucleic Acids Res. 2000 January 1; 28(1): 380–382.</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-20205385673609255582007-05-24T09:05:00.000-07:002007-05-24T10:04:25.360-07:00NCBI course - Principles of PubChemhttp://www.ncbi.nlm.nih.gov/Class/PubChem/course.html<br />ftp://ftp.ncbi.nih.gov/pub/PowerTools/PubChem/Docs/handout.pdf<br />http://www.ncbi.nlm.nih.gov<br />http://pubchem.ncbi.nlm.nih.gov<br />http://www.mli.nih.gov/mlsmr/index.php<br /><br />What is PubChem?<br />A public repository of electronic representations of small molecules and associated bioactivity assay data<br />- new program -- link chem informatics to bio-informatics<br />- A component of the NIH Molecular Libraries RoadMap<br />- Part of the NCBI <span style="font-weight: bold;">Entrez </span>search and linking system<br />- A system of four components: molecular libraries<br />--PubChem Substance DB<br />--PubChem Compound DB<br />--PubChem BioAssay DB<br />--PubChem Structure Search / tool like blast / vast<br /><br />http://nihroadmap.nih.gov/ --> Grants<br />compund repository (MLSMR)<br /><a href="http://mlsmr.discoverypartners.com/">molecular libraries small molecule repository</a><br />molec lib screening center netwk MLSCN<br />predictive ADMET<br /><br /><span style="font-weight: bold;">The </span>National Center for Biotechnology Information<br />What does NCBI do?<br />Accepts submissions of primary data. <br />Develops tools to analyze these data. <br />Uses these tools to create derivative databases based on the primary data. <br />Provides free search, linking, and retrieval of data, mainly through the Entrez system.<br /><br /><span style="font-weight: bold;">entrez - text / seq - blast / protein stru - vast / sm molec struc - pubchem</span><br /><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">pubchem Types of Databases</span><br />=Primary Databases<br />Original submissions by experimentalists<br />Content controlled by the submitter<br />Examples: GenBank, SNP, GEO, PubChem Substance and BioAssay<br />=Derivative Databases<br />Built from primary data<br />Content controlled by third party (NCBI)<br />Examples: RefSeq, RefSNP, GDS, PubChem Compound<br /><br /><span style="font-weight: bold;">PubChem Databases<br /></span>substance = real chemicals / non redundant<br />bioassay = experimental<span style="font-weight: bold;"></span><br /><br /><span style="font-weight: bold;">PC Substance Record</span><br />structure display / subID = sid + [compund id=cid] / link to depositor / chem nomenclature<br />? (iupac names from ncbi)<br /><br />Non-uniformity in PC Substance - diff ways to draw a chemical<br />The Bizarre / non-standard in PC (pubchem) Substance (chamomile tea, grapefruit)<br /><span style="font-weight: bold;"><br />PubChem Compound </span><br />Standardize Structures<br />Verify Chemical Data<br />Atom description (label, element)<br />Functional group clean-up<br />Atom valence verification to prevent non-sense structures<br />“Normalize” and “Standardize”<br />Valence-Bond canonicalize (for Tautomer invariance)<br />Aromaticity detection and self- consistency<br />Stereochemistry detection<br />Explicit hydrogen assignment<br />Structural Representations<br />2D Coordinate generation<br />Images created<br />Structures that fail to standardize…<br />Have no records in PC Compound<br />Cannot be searched by structure<br /><br />Stereoisomers in PC Compound (chiral sugars)<br /><br /><span style="font-weight: bold;">PubChem Compound continued</span><br />- Calculate Properties and Links<br /> Nomenclature<br />IUPAC http://www.iupac.org/<br />SMILES & SMARTS<br />InChI<br />- Structural Information<br />Calculate & store “Fingerprints”<br />Calculate & link to similar structures (90% level)<br />- Physical Properties<br />Molecular Formula<br />Molecular Weight<br />Number of H-bonds donor/acceptor sites<br />XLogP value<br />Lipinski value (bioavailability)<br />Number of Rotatable bonds<br />- Links to NCBI Database Records<br />Structures (MMDB records) http://130.14.29.110/Structure/MMDB/mmdb.shtml<br />Protein sequences (from Structure links)<br />Genes (from Protein links)<br />- Links to MeSH Terms through IUPAC name<br />("believe it or not, but people read every article and assign mesh to them" ... :-)<br /><br /><span style="font-weight: bold;">PC Compound Record - all the data, most complete</span><br />1 CID / bioactivity / links to substances<br /><span style="font-size:130%;"><span style="font-weight: bold; color: rgb(255, 0, 0);">2 MeSH Links - use pubchem to do chem medline searches!</span></span><br /><span style="font-weight: bold;">3 Calculated Properties</span><br />vendors / descriptors<br /><br /><span style="font-weight: bold;">Handling Mixtures</span><br />SID / CID / links to unique components & their cid's<br /><br /><span style="font-weight: bold;">PC BioAssay Record</span><br />Tables - active etc / overlap made non redundant<br /><br /><span style="font-weight: bold;">BioAssay Protocol</span><br />methods / procedures - no std's / text explanations & links to web<br /><br />PubChem integration in Entrez<br />-What is Entrez?<br />-System of 31 linked databases<br />-Text search engine<br />-Tool for finding biologically linked data<br />-Data retrieval engine<br />-Virtual workspace for manipulating large datasets<br />-Free public access<br /><br /><span style="font-weight: bold;">Entrez review</span><br />Fields<br /><span style="color: rgb(51, 102, 255);">chemical[synonym] (all)<br /></span><span style="color: rgb(51, 102, 255);">chemical[completesynonym] (exact)<br />Atom abrev[element]<br />[sourcename]<br />[filter] = structure, rules<br />lipinski[filter]<br />[pharmaction] = mesh<br /><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">pubchem Search page</span><br /></span><span style="font-weight: bold;">Entrez Limits page, very diff from medline</span><br />Details<br />Preview/Index<br />Entrez History<br /><br /><span style="font-weight: bold;">Display - Downloading Reports</span><br />- property report - one line<br /><span style="color: rgb(51, 102, 255);">- BULK -- pubchen download - long records, goes to a URL for a week</span><br /><br /><span style="font-weight: bold;">Linking in Entrez</span><br />- hard = biol / chem<br />- soft = computed, algorhithm links<br /><br /><span style="font-weight: bold;">PubChem Links</span><br />related struct / assays / literature (pmc = free) / other entrez db<br /><br /><span style="font-weight: bold;">Linking in Bulk</span><br />Use DISPLAY link for list --> "pubchem bioassays" ...<br /><br /><span style="font-weight: bold;">The PubChem FTP Site</span><br />ftp://ftp.ncbi.nih.gov/pubchem<br /><br /><span style="font-weight: bold;">Programming Tools</span><br /><br /><span style="font-weight: bold;">PubChem Help -- excellent<br /></span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-76916973982848106682007-05-21T10:37:00.000-07:002007-06-21T11:42:44.366-07:00NCBI New Database -- Protein Clusters<span style=";font-family:arial;font-size:100%;" ><span style="">Protein Clusters is a </span></span><span style=";font-family:arial;font-size:100%;" >collection of related protein sequences (clusters). These clusters consist of Reference Sequence (ie, RefSeq = </span><span style="font-size:100%;"><span style="font-family:arial;">comprehensive, integrated, non-redundant sets of sequences)</span></span><span style=";font-family:arial;font-size:100%;" > proteins which are encoded by prokaryotic and chloroplastic <a href="http://en.wikipedia.org/wiki/Plasmid">plasmids </a>and genomes. </span><span><span style=";font-family:Verdana;font-size:85%;" > </span></span><br /><br /><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=proteinclusters">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=proteinclusters</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-68071733300239883592007-05-18T09:10:00.000-07:002007-05-18T09:10:46.697-07:00NCBI Genes and Disease PageThis resource is aimed at consumer health needs, but its generic information about genetic diseases might be useful to the student researchers. It has splendid links to other NCBI resources such as OMIM.<br /><a href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2">http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2</a><br /><br />An amusing NCBI taxonomy site has extinct critter's DNA:<br /><a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=extinct">http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=extinct</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-6024894348816074002007-05-17T10:56:00.000-07:002007-05-17T10:58:37.981-07:00Seminar - May 23 - noon-2:00The Genomics Shared Service presents:<br />Empowering Genomic Discoveries with Agilent Microarray Platform<br /><br />Agilent Technologies is at the forefront of integrated genomics, offering solutions for gene expression profiling, miRNA, chromosomal copy number detection (CGH), transcription factor binding (ChIP-chip), methylation, alternative splicing and informatics. Learn how advancements with Agilent’s inkjet printing flexibility and free online design tools can be leveraged to further enable the research community at the University of Arizona.<br /><br />Speaker: Christopher Hopkins, Ph.D. Agilent Technologies<br />Location: Kiewit Auditorium, Arizona Cancer Center<br />Date: Wednesday, May 23, 2007<br />Time: Noon 2 p.m., LUNCH WILL BE PROVIDED.<br /><br />Come see what the latest addition to the Genomics Shared Service can do<br />for your research.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1083941841132583295.post-6853710549838270012007-05-17T09:47:00.001-07:002007-05-17T09:47:32.050-07:00Seminar - May 24 at 8amThe College of Medicine invites you to attend the special seminar of Dr.<br /> Lisa Rimsza, who will be visiting the University of Arizona as a candidate<br /> for the Head of Pathology. Please join us for this exciting presentation!<br /><br /> COLLEGE OF MEDICINE SPECIAL SEMINAR<br /> Thursday, May 24: 8:00 - 9:00am<br /> College of Medicine, room 8403<br /> Translational Research in Lymphoma: Using Gene Expression Profiling to<br /> Find and Expose "Immunostealth"Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1083941841132583295.post-87712580699411915332007-05-15T08:27:00.000-07:002007-05-15T09:48:46.466-07:00NCBI: Microbial Genome Notes - morning<span style="font-weight: bold; color: rgb(204, 0, 0);">Hand-out</span><br /><a href="ftp://ftp.ncbi.nih.gov/pub/minicourses/CURRENT/HO/PDF/Microbial.pdf">ftp://ftp.ncbi.nih.gov/pub/minicourses/CURRENT/HO/PDF/Microbial.pdf</a><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">Primary page</span><br /><a href="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi">http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi</a><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">NCBI -- <a href="http://www.ncbi.nlm.nih.gov/">http://www.ncbi.nlm.nih.gov/ </a>-- Instructors</span><br />Susan Dombrowski / Wayne ....<br /><span style="color: rgb(255, 102, 102);">Help</span><br />blast-help@ncbi.nlm<br />301-496-2475<br /><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">Outline</span><br />Entrez / pubmed & MynNCBI / BLAST / spec resources<br /><span style="font-weight: bold; color: rgb(255, 102, 102);">Use</span><br />Entrez >> subject / text<br />BLAST >> sequence / pcr reaction --<a href="http://www.ncbi.nlm.nih.gov/BLAST/"> http://www.ncbi.nlm.nih.gov/BLAST/</a><br /><span style="color: rgb(255, 102, 102);">Entrez</span><br />PubMed / taxonomy (lineage) / VAST / BLAST / Phylogeny<br />interlinked - related sequences btw db<br />neighboring - inside a db<br />30 db -- new Protein Clusters (UniGene for protein)<br />Groups -- nucleotides / pubmed / taxonomy / proteins<br />-- Search _ all[filter]_ = current content of db<br /><span style="color: rgb(255, 102, 102);">Types of db</span><br />primary db (orig data, controlled by submitter)<br />derived db (blt from primary, controlled by ncbi)<br /><span style="color: rgb(255, 102, 102);">Searching</span><br />Help manual in entrez books - <a href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpbook.TOC">http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpbook.TOC</a><br />All db / cross db -- <a href="http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi">http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi</a><br />default = search everywhere<br /><span style="font-weight: bold;">Tabs </span>= limit (fields, preview index)<br />[orgn] = organism field<br />entry Number = code<br />XM = experimental<br />icon -<br /><span style="color: rgb(255, 102, 102);">MyNCBI</span><br />SDIs / "google alerts"<br /><span style="color: rgb(204, 0, 0); font-weight: bold;">BLAST - <a href="http://www.ncbi.nlm.nih.gov/BLAST/">http://www.ncbi.nlm.nih.gov/BLAST/</a></span><br />"basic local alignment search tool"<br />- very basic BLAST! >> no scoring, no statistics<br />- local, isolated, surprising reguions of similarity<br />- breaks seq into words<br />- hits become "seed" for alignment extension<br />- search algorithms .. smith-waterman - "local alignment"<br />- global alignment - end to end for pockets of similarity<br />- local alignment - matches letter by letter, not sequence by sequence (?) .... <a href="http://en.wikipedia.org/wiki/Local_alignment">http://en.wikipedia.org/wiki/Local_alignment</a><br />- word size in nuc = exact match<br />- word size in proteins -- flexible matching (exact or "neighbohood words" - amino acid residues that are similar / biochem equiv) -<br />NR = non redundant protein = default db<br />LIMITS - organism<br />To exclude = _all[filter] NOT mammals_<br />Algorithm parameters - higher Expect Value, lower stringency<br />short sequence strategy ....<br />long sequence strategy (eval high<br /><span style="color: rgb(255, 102, 102);">Precomputed services</span><br />- nuc or prot = related sequences<br />- blast link = Blink (like related sequences)<br />- transcript clusters = UniGene<br />- protein homologs = Homologene<br /><span style="color: rgb(255, 102, 102);">DBS<br /><span style="color: rgb(0, 0, 0);">Nucleotide</span></span> -- Links / Related == can Sort Related Sequences - chose how<br />Genbank - No protein sequences<br />Protein >> BLink = related prot seques<br />Genome >> book links, many seque pub as texts<br />-- shotgun: <a href="http://www.ncbi.nlm.nih.gov/Genbank/wgs.html">http://www.ncbi.nlm.nih.gov/Genbank/wgs.html</a><br />-- browse genome trees<br /><br /><span style="font-weight: bold; color: rgb(204, 0, 0);">Bits</span><br />GC=<b>guanine-cytosine content</b> (<b>GC-content</b>) is a characteristic of the genome of any given organism --<a href="http://en.wikipedia.org/wiki/Organism" title="Organism"> http://en.wikipedia.org/wiki/GC-content</a><br /><br /><span style="color: rgb(204, 0, 0); font-weight: bold;">Ideas</span><br />MyNCBI set up for Bio5 researchers<br />(Elvis lives .. short sequence stragey)Unknownnoreply@blogger.com0