tag:blogger.com,1999:blog-51691857152289131872024-02-06T21:19:49.727-08:00Integrative Bioinformatics LaboratoryIntegrated data management and analysis to put the systemic puzzle together (for more see <a href=http://integrativebioinformatics.blogspot.com/2007/03/who-are-we.html><u>Mission</u></a>)Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.comBlogger50125tag:blogger.com,1999:blog-5169185715228913187.post-24834402557695771032008-02-26T08:59:00.000-08:002008-02-26T09:15:16.855-08:00Integrative Bioinformatics 13<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="COLOR: rgb(153,51,0)"><strong>February 26 - GUI example 1 / 4 : The Cancer Genome Project<br /></strong></span></p><p> </p><p> </p><p></p><p></p><p></p><p><br /></p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com1tag:blogger.com,1999:blog-5169185715228913187.post-64676608340393651532008-02-21T12:41:00.000-08:002008-02-21T13:19:39.394-08:00Integrative Bioinformatics 12<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="color: rgb(153, 51, 0);"><strong>February 21- Standards<br /></strong></span></p>Link to the presentation can be found <a href="http://ibl.mdanderson.org/rppaml/class/howto_standards.pdf">here</a><p> </p><p> </p><p> </p><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-5100297351082194802008-02-19T09:18:00.000-08:002008-02-19T14:14:56.327-08:00Integrative Bioinformatics 11<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="COLOR: rgb(153,51,0)"><strong>February 19 - Homework review: UCSC data service API</strong></span></p><ul><li><span style="COLOR: rgb(0,0,153)">Diogo Veiga - using Distributed Annotation System (<a href="http://www.biodas.org/wiki/Main_Page">DAS</a>)</span></li></ul><p><span style="color:#000099;">- The reference report was published at <a href="http://www.biomedcentral.com/1471-2105/8/333">http://www.biomedcentral.com/1471-2105/8/333</a>.<br />-</span><span style="color:#000099;"> Affymetrix <a href="http://www.affymetrix.com/support/developer/tools/IGB_User_Guide.pdf">Integrated Genome Browser</a>.<br />- <a href="http://www.genboree.org/">GenBoree</a> at Baylor uses DAS.<br />- <a href="http://biodas.org/documents/das2/das2_protocol.html">DAS 2</a> was released in 2007 and supprots both retrieval and submission.<br />- <a href="http://www.dasregistry.org/course.jsp">DAS workshop 2008</a>.</span></p><ul><li><span style="color:#000099;">Helena Deus - hacking Web 1.0 pages.</span></li></ul><p> </p><p> </p><p></p><p> </p><p> </p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-31030125523550439042008-02-19T09:00:00.000-08:002008-02-19T09:17:15.907-08:00The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology<a href="http://http://www.biomedcentral.com/1471-2105/9/86">http://www.biomedcentral.com/1471-2105/9/86</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-61736223915394362992008-02-12T08:22:00.000-08:002008-02-14T11:06:34.483-08:00Integrative Bioinformatics 10<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="color: rgb(153, 51, 0);"><strong>February 12,14 - S3DB, a distributed semantic DBMS</strong></span></p><ol><li><span style="color: rgb(0, 0, 153);">Why - hurting enough already?</span></li><li><span style="color: rgb(0, 0, 153);">What - simultaneous annotation of usage and content weaved into a permission management model.</span></li><li><span style="color: rgb(0, 0, 153);">How - RESTful API.</span></li></ol><p><span style="color: rgb(0, 0, 153);">Individual accounts will be created in class. You can also download your own at <a href="http://www.s3db.org/">http://www.s3db.org/</a>. Additional documentation can also be found <a href="http://s3db.wikidot.com/">here</a>.</span></p><p><span style="color: rgb(0, 0, 153);">The N3 notation for RDF is VERY instructive, have a look <a href="http://www.w3.org/2000/10/swap/Primer">here</a>.</span></p><p><span style="color: rgb(0, 0, 153);"></span></p><p><span style="color: rgb(0, 0, 153);">For complete documentation on RDF the right place to go is the source, <a href="http://www.w3.org/RDF/">W3C's reference documentation</a>.</span></p><p><span style="color: rgb(0, 0, 153);">example of public RDF browser: <a href="http://simile.mit.edu/welkin/">Welkin</a>.</span></p><p><span style="color: rgb(0, 0, 153);">example of commercial RDF browser: <a href="http://www.io-informatics.com/products/sentient-KE.html">Sentient</a>.</span></p><p><span style="color: rgb(0, 0, 153);">Function for building S3QL queries: </span><a style="color: rgb(0, 0, 153);" href="http://ibl.mdanderson.org/%7Emhdeus/S3QLSyntax.m">S3QLSyntax</a><br /></p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-52768716154924282822008-02-05T08:47:00.000-08:002008-02-05T08:54:25.481-08:00BioDas article for Feb 12 Lab Meeting<span style="color: rgb(0, 0, 153);">Integrative genomics using DAS : <a href="http://www.biomedcentral.com/1471-2105/8/333">http://www.biomedcentral.com/1471-2105/8/333</a></span>Diogohttp://www.blogger.com/profile/04303942649141836384noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-40673644795137004242008-02-05T08:29:00.001-08:002008-02-07T08:55:03.044-08:00Integrative Bioinformatics 9<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="COLOR: rgb(153,51,0)"><strong>February 7 - more on Graphic User Interfaces</strong></span></p><ol><li><span style="COLOR: rgb(0,0,153)">Practice of GUI development in Matlab:<br />a) how to find the handles<br />b) how to change attribute, value pairs<br />c) guihandles and related commands</span></li><li><span style="color:#000099;">BIODAS as a tool for integration - Ana's challenge: <a href="http://dils2008.lri.fr/index.php?option=com_content&task=view&id=16&Itemid=30">DILS 2008</a>.</span></li></ol>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-66032551472198426122008-01-31T08:48:00.000-08:002008-01-31T09:06:24.055-08:00Integrative Bioinformatics 7<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="COLOR: rgb(153,51,0)"><strong>January 31 - Review of homework assignments - dynamic programming for sequence alignment and regular expressions:</strong></span></p><p></p><ol><li><span style="COLOR: rgb(0,0,153)">Dynamic programming of Needleman-Wunch alignment algorithm.</span></li><li><span style="COLOR: rgb(0,0,153)">Review of solutions to other alignment algorithms, note storing matrix indexes for traceback proceedures.</span></li><li><span style="COLOR: rgb(0,0,153)">Visualization of scoring dynamic programming matrices.</span></li><li><span style="color:#000099;">Regular expression for tag delimitation in tabular formats.</span></li><li><span style="color:#000099;">Regular expression chalange.</span></li><li><span style="color:#000099;">Recommended new reading - upcomming chalanges/opportunities in sequence analysis:<br /><br /><a href="http://www.blogger.com/A%20Plan%20to%20Capture%20Human%20Diversity%20in%201000%20Genomes">A Plan to Capture Human Diversity in 1000 Genomes</a> [Science 25 January 2008]<br /><a href="http://sciencenow.sciencemag.org/cgi/content/full/2008/124/3">Scientists Synthesize a Genome From Scratch</a> [ScienceNOW Daily News24 January 2008]<br /></span></li></ol><p><span style="COLOR: rgb(153,0,0)"><strong>HOMEWORK<br /></strong></span><span style="COLOR: rgb(153,0,0)">(note old solutions at <a href="http://ibl.mdanderson.org/~jalmeida/IB2008/">http://ibl.mdanderson.org/~jalmeida/IB2008/</a>)</span></p><p>Write you favorite implementation of a UCSC client in matlab and include with your m-files a archive html report describing its use, produced with cell programming + publish.</p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-51577374422674886102008-01-29T08:56:00.000-08:002008-01-29T09:51:27.398-08:00Integrative Bioinformatics 6<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="color: rgb(153, 51, 0);"><strong>January 24 - hands on session developing a client for UCSC Genome Browser (everybody):</strong></span></p><p></p><ol><li><span style="color: rgb(0, 0, 153);">BioDAS (Diogo)</span></li><li><span style="color: rgb(0, 0, 153);">Review of interoperable solutions.</span></li><li><span style="color: rgb(0, 0, 153);">Introduction to the Document Object Model (DOM) and how it can be mapped into a regular data structure using XML. See for example Matlab's <a href="http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/access/helpdesk/help/techdoc/ref/xmlread.html&http://www.google.com/search?q=mathworks+xmlread&rls=com.microsoft:en-us&ie=UTF-8&oe=UTF-8&startIndex=&startPage=1">XMLREAD</a> command and compare it with <a href="http://www.geodise.org/toolboxes/generic/xml_toolbox.htm">this tool box</a>.</span></li></ol><p><span style="color: rgb(0, 0, 153);">Integrative genomics using DAS : <a href="http://www.biomedcentral.com/1471-2105/8/333">http://www.biomedcentral.com/1471-2105/8/333</a></span></p><p><span style="color: rgb(153, 0, 0);"><strong>HOMEWORK</strong></span></p><p>Don't forget pending assignments: Write matlab function that reads HTML table into cell array and also the alignment homework. This is due Thursday,.</p><br /><p><br /><span style="color: rgb(204, 0, 0);">Biodas queries against UCSC Genome Database</span><br /><br />%% Data sources command<br /><br />%Get all genomes (data sources) available. XML looks like this:<br />% <dasdsn><br />% <dsn><br />% <source id="hg18" version="1.00">Mar. 2006 at UCSC</source><br />% <mapmaster>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg18</mapmaster><br />% <description>Human Mar. 2006 Genome at UCSC</description><br />% </dsn><br />% ...<br />% <dsn><br /><br />% this code is for manipulating using DOM API<br />genomes_Dom = xmlread('http://genome.ucsc.edu/cgi-bin/das/dsn');<br />dsnL = genomes_Dom.getElementsByTagName('DSN');<br />sourceL = genomes_Dom.getElementsByTagName('SOURCE');<br />descrL = genomes_Dom.getElementsByTagName('description');<br /><br />% this is code for manipulating using XML Toolbox from Geodise (download it first)<br />xml = urlread('http://genome.ucsc.edu/cgi-bin/das/dsn');<br />t_parseany = xml_parseany(xml);<br /><br />%when comes to a leave, use this:<br />t_parseany.DSN{1}.SOURCE{1}.ATTRIBUTE(1)<br />t_parseany.DSN{1}.SOURCE{1}.CONTENT<br /><br />%% entry_points command<br /><br />%Get all chromosomes (entry_points command). Here, hg16 refers to a specific genome assembly (Human Genome July 2003), as returned w/ the data source command.<br />%eg.<br />urlread('http://genome.ucsc.edu/cgi-bin/das/hg16/entry_points')<br /><br />%% types command<br /><br />%Get annotation types for a sequence segment. Annotation types are all features annotated for sequence, as knownGenes, snps, mRNAs, ESTs, exons, introns and so on.<br />%This command give us a overview of the annotation for the sequence, including the number of each feature. XML looks like this:<br />urlread('http://genome.ucsc.edu/cgi-bin/das/hg16/types?segment=4:3000000,4000000');<br /><br />%% types command with parameters<br /><br />%Get one or more specific features for sequence. Several features and/or segments can be queried at same time.<br />%eg. Retrieve all SNPs and identified genes for the segment.<br />urlread('http://genome.ucsc.edu/cgi-bin/das/hg16/features?segment=4:3000000,4000000;type=snp;type=knownGene');<br /><br />%% dna command<br /><br />%Get raw nucleotide sequence data.<br />urlread('http://genome.ucsc.edu/cgi-bin/das/hg16/dna?segment=chr4:30000,300100');<br /><br /><br /><br /><br /><br /><br /></p><p><br /></p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com1tag:blogger.com,1999:blog-5169185715228913187.post-36759935619610050622008-01-29T08:43:00.000-08:002008-02-04T12:39:58.098-08:00list of algorithms for copy number aberration<p class="MsoNormal" style="margin-left: 0.25in; text-indent: -0.25in; font-weight: bold; color: rgb(0, 0, 153);"><!--[if !supportLists]--><span style="font-size:100%;"><span style="">1.<span style=""> </span></span>Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays. <a href="http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pgen.0030143">http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pgen.0030143</a><o:p></o:p></span><!--[endif]--></p> <p class="MsoNormal" style="margin-left: 0.25in; text-indent: -0.25in; font-weight: bold; color: rgb(0, 0, 153);"><!--[if !supportLists]--><span style="font-size:100%;"><span style="">2.<span style=""> </span></span>Computation of recurrent minimal genomic alterations from array-CGH data <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/7/849">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/7/849</a><o:p></o:p></span><!--[endif]--></p> <p class="MsoNormal" style="margin-left: 0.25in; text-indent: -0.25in; font-weight: bold; color: rgb(0, 0, 153);"><!--[if !supportLists]--><span style="font-size:100%;"><span style="">3.<span style=""> </span></span>STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments<o:p></o:p></span><!--[endif]--></p> <p class="MsoNormal" style="font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><span style=""> </span><a href="http://www.genome.org/cgi/content/abstract/gr.5076506v1">http://www.genome.org/cgi/content/abstract/gr.5076506v1</a><o:p></o:p></span></p> <p class="MsoNormal" style="margin-left: 0.25in; text-indent: -0.25in; font-weight: bold; color: rgb(0, 0, 153);"><!--[if !supportLists]--><span style="font-size:100%;"><span style="">4.<span style=""> </span></span>SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets<o:p></o:p></span><!--[endif]--></p> <p class="MsoNormal" style="font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><span style=""> </span><a href="http://www.biomedcentral.com/content/pdf/1471-2105-8-422.pdf">http://www.biomedcentral.com/content/pdf/1471-2105-8-422.pdf</a><o:p></o:p></span></p> <p class="MsoNormal" style="font-weight: bold; color: rgb(0, 0, 153);"><!--[if !supportLists]--><span style="font-size:100%;"><span style="">5.<span style=""> </span></span></span><span style="font-size:100%;">A Robust Algorithm for Copy Number Detection Using High-Density Oligonucleotide Single Nucleotide Polymorphism Genotyping Arrays<o:p></o:p></span><!--[endif]--> </p><p class="MsoNormal" style="font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><span style=""> </span><a href="http://cancerres.aacrjournals.org/cgi/content/abstract/65/14/6071">http://cancerres.aacrjournals.org/cgi/content/abstract/65/14/6071 </a></span><br /></p><p class="MsoNormal" style="font-weight: bold; color: rgb(0, 0, 153);">6. Modeling recurrent DNA copy number alterations in array CGH data<br /></p> <p class="MsoNormal" style="text-indent: 24pt; font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><span style=""> <span style="font-weight: bold;"> </span></span><span style="font-size:100%;"><a style="font-weight: bold;" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i450">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i450</a></span></span></p><p class="MsoNormal" style="text-indent: 24pt; font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><o:p></o:p><span style=""><br />7.<span style=""> </span></span>Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis<o:p></o:p><a href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.215?journalCode=c%20%20%20%20%20%20mb"><br /></a></span></p><p class="MsoNormal" style="text-indent: 24pt; font-weight: bold; color: rgb(0, 0, 153);"><span style="font-size:100%;"><a href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.215?journalCode=c%20%20%20%20%20%20mb">http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.215?journalCode=cmb<br /></a></span></p><span style="color: rgb(51, 51, 255);font-size:100%;" ><br /></span><span style="font-weight: bold; color: rgb(0, 0, 153);font-size:100%;" ><span style="">8. Assessing the significance of chromosomalaberrations in cancer: Methodology and application to glioma<br /><br /></span></span> <p class="MsoNormal" style=""> </p><span style="font-size:100%;"><a style="font-weight: bold;" href="http://www.pnas.org/cgi/content/full/104/50/20007"><span class="MsoHyperlink">http://www.pnas.org/cgi/content/full/104/50/20007</span></a></span><p class="MsoNormal" style=""><br /><span class="MsoHyperlink"><span style="font-size:12;"></span><o:p></o:p></span></p> <p class="MsoNormal" style="text-indent: 24pt; font-weight: bold; color: rgb(0, 0, 153);"><br /></p><p class="MsoNormal" style="text-indent: 24pt; font-weight: bold; color: rgb(0, 0, 153);"><br /><span style="font-size:100%;"><o:p></o:p></span></p>Chunyan Caihttp://www.blogger.com/profile/09045501817516422547noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-43259536953981099232008-01-29T08:28:00.000-08:002008-01-29T08:32:02.477-08:00Data analysis and bioinformatics tools for tandem mass spectrometry in proteomicslink to<br /><h2><span style="font-size:85%;"><a href="http://physiolgenomics.physiology.org/cgi/content/abstract/00298.2007v1"> Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics</a></span></h2>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-47289884405181274602008-01-29T08:27:00.001-08:002008-01-29T08:32:17.353-08:00PRIDE: the proteomics identifications database.link to<br /><h2><span style="font-size:85%;"><a href="http://www.ncbi.nlm.nih.gov/pubmed/16041671">PRIDE: the proteomics identifications database.</a></span></h2>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-27962651709272453812008-01-28T12:55:00.000-08:002008-01-28T13:01:09.847-08:00Flexible Informatics for Linking Experimental Data to Mathematical Models Via DataRail<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn018v1">Link to Bioinformatics Paper</a><br /><br />ABSTRACT<br />Motivation: Linking experimental data to mathematical models in<br />biology is impeded by the lack of suitable software to manage and<br />transform data. Model calibration would be facilitated and models<br />would increase in value were it possible to preserve links to training<br />data along with a record of all normalization, scaling, and fusion<br />routines used to assemble the training data from primary results.<br />Results: We describe the implementation of DataRail, an open<br />source MATLAB-based toolbox that stores experimental data in<br />flexible multi-dimensional arrays, transforms arrays so as to maximize<br />information content, and then constructs models using internal<br />or external tools. Data integrity is maintained via a containment hierarchy<br />for arrays, imposition of a metadata standard based on a<br />newly proposed MIDAS format, assignment of semantically typed<br />universal identifiers, and implementation of a procedure for storing<br />the history of all transformations with the array. We illustrate the<br />utility of DataRail by processing a newly collected set of ~22,000<br />measurements of protein activities obtained from cytokinestimulated<br />primary and transformed human liver cells.<br />Availability: DataRail is distributed under the GNU General Public<br />License and available at http://code.google.com/p/sbpipeline/<br />Contact: sbpipeline@hms.harvard.edu<br />Supplementary information: accompanies this paper.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-28109998051551046632008-01-24T08:45:00.000-08:002008-01-24T08:51:37.225-08:00Integrative Bioinformatics 5<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="color:#993300;"><strong>January 24 - hands on session developing a client for UCSC Genome Browser (everybody):</strong></span></p><p></p><ol><li><span style="color:#000099;">Quick introduction to REST vs SOAP + revisit precedent CORBA, EMAIL, port chanelling etc</span></li><li><span style="color:#000099;">Quick Introduction to upcomming data base and computational statistics modules.</span></li><li><span style="color:#000099;">Hands on session</span>.</li></ol><p><span style="color:#990000;"><strong>HOMEWORK</strong></span></p><p>Don't for get last sessions's: Write matlab function that reads HTML table into cell array.</p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-12609273837516342892008-01-22T08:43:00.000-08:002008-01-22T10:22:09.317-08:00Integrative Bioinformatics 4<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p><span style="color:#993300;"><strong>January 22 - Data structures and data services (Pablo, Jonas):</strong></span></p><p></p><ol><li>Extracting data structures from data services.</li><li>Attribute/Value pairs --> XML --> RDF tripples</li><li><a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/regexp.html">Regular Expressions</a>.</li><li><a href="http://genome.ucsc.edu/">UCSC Genome browser </a>as a data service providing an aggragating data structure. For online tutorials see <a href="http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml">this page</a>.</li></ol><p><span style="color:#990000;"><strong>HOMEWORK</strong></span></p><p>Write matlab function that reads HTML table into cell array.</p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-76262167138306179462008-01-17T08:43:00.000-08:002008-01-17T08:48:55.449-08:00Integrative Bioinformatics 3<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p></p><p>1. Discussion of matrix notation using teh homework assignment. [<a href="http://ibl.mdanderson.org/~jalmeida/lixo/max_.m">my solution</a>].</p><p>2. Alignment as a similarity metric. [<a href="http://ibl.mdanderson.org/~jalmeida/lixo/Sequence_Alignment_I.ppt">Presentation</a>].</p><p>3. Discussion of collective assignment on developing a client that will use UCSC Genome Browser as a data service.</p><p>HOMEWORK</p><p>Since you did so well in the introductory class, today we move to an advance algorithm deployment assignment. The Homework is described in the last slide of the presentation.</p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-273622045738910042008-01-15T05:40:00.000-08:002008-01-15T05:49:39.979-08:00Integrated Bioinformatics 2008 2<p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a> ]</p><p></p><p>This class will introduce the two main components of the integrative exercise: data structures and programming languages. The exploration of these two topics will be pursued in MATLAB, a fast prototyping scientific and engineering programming environment.</p><p>In addition to the very extensive help material that comes with MATLAB (from manuals to viodeos, clisck on "Help" in the top menu to find more), Mathworks' website also includes a great selection of <a href="http://www.mathworks.com/company/events/archived_webinars.html">webminars</a>.<br /></p><p>HOMEWORK</p><p>Today we have a small homework assignment just to make sure we all know how to send them to me: write a m-function that identifies the largest element of a matrix and return their location.</p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-41556521656224917662007-11-26T21:26:00.000-08:002007-11-26T21:33:40.611-08:00Upcoming event: 2007 Computational & Theoretical Biology Symposium: Dec. 7-9 at Rice UniversityHey folks,<br /><br /> it's worthy to check, the registration is free and the speakers will be talking about interested topics. I just don't know why they're making it in the week before the finals, including at Rice...<br /><br /><br />************************<br /><br />We would like to invite you to attend the 4th annual Computational &<br />Theoretical Biology Symposium at <span class="nfakPe">Rice</span> University. It will be held from<br />December 7 - 9 and features invited talks of more than 20 speakers from<br />leading institutions across the US. Participants at this annual<br />symposium will gain new insights into a variety of approaches in<br />theoretical methods of statistical mechanics, nonlinear dynamics, and<br />systems biology that are being developed and applied to study and<br />manipulate nature.<br /><br /><br /><br />Admission to the symposium is free and open to everyone; registration is<br />not required. To learn more about the hosts/venue, program and invited<br />speakers, visit <a href="http://ctbs.rice.edu/" target="_blank">http://ctbs.<span class="nfakPe">rice</span>.edu</a> <<a href="http://ctbs.rice.edu/" target="_blank">http://ctbs.<span class="nfakPe">rice</span>.edu/</a>> .<br /><br /><br /><br />Student and Postdoc participants are encouraged to present in a poster<br />session to be held on Saturday, December 8th from 1:00 - 2:30 pm and<br />during the coffee break. Presenters are asked to send an e-mail to<br /><a href="mailto:ctbs@mailman.rice.edu">ctbs@mailman.<span class="nfakPe">rice</span>.edu</a> <<a href="http://ctbs.rice.edu/ctbs@mailman.rice.edu" target="_blank">http://ctbs.<span class="nfakPe">rice</span>.edu/ctbs<wbr>@mailman.<span class="nfakPe">rice</span>.edu</a>> with<br />poster details by Thursday, November 29th so that logistical<br />arrangements can be made.<br /><br /><br /><br />Best Regards,<br /><br />Symposium Organizing CommitteeDiogohttp://www.blogger.com/profile/04303942649141836384noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-51103130977720707012007-11-17T13:26:00.000-08:002007-11-17T13:41:14.632-08:00Lynn Vogel talks about MDAnderson IT infrastructure.<a href="http://www.enterpriseleadership.org/listen/podcast-vogel">http://www.enterpriseleadership.org/listen/podcast-vogel</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-37581200643695858862007-05-28T18:30:00.000-07:002007-07-16T21:53:47.469-07:00AMIA 2007 Spring Congress SynopsisThis year's <a href="http://www.amia.org/meetings/s07/">AMIA Spring Congress</a> involved researchers from many fields including Medical Communities, Nurses, Informatics, Basic Research (bench) and some industry representatives as well, all coming together with a common goal: translate biomedical knowledge into medical practice. The meeting included 5 tracks, spanning from nursing informatics to clinical decision support, personalized health records and translational research, so it was a good mix of several domains each with its own challenges and methodologies.<br />Adam Bosworth, vice-president of Google opened the meeting with a blast, his vision on how health related information will/should be handled in a not so distant future was mesmerizing, his insight on how google is prepared to adress this challenge an unexpected surprise. Here are <span style="FONT-WEIGHT: bold"><a href="http://64.233.179.110/blog_resources/Bosworth_AMIA_May07.pdf">his notes</a></span>.<br />The <a href="http://www.amia.org/meetings/s07/track_tri.asp">translational research informatics track</a> was one of the most interesting, it became clear how CTSA has had and is still having a key role in the development of a <span style="FONT-STYLE: italic">new science</span> - Integrative Bioinformatics. Several CTSA awardees made their voices heard and lots of ideas flew around the room, from tools already being developed and evaluated to tools promising but still in the planning process, integration was the keyword and the main challenge.<br />caBIG was also given a chance to give their 2 cents, but the most enthusiastic seemed to rely mostly on in-house costumized tools. There were plenty of semantic web technologies aficionados, including users of Protege, but no Semantic or Sloppy Databases (exept ours :D).<br />Christopher Chute also made his presence felt, his insight in what regards the basic researchers vs clinical research "Chasm of Semantic Despair" was particularly insightfull.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-21007896380972065802007-05-15T04:28:00.000-07:002007-05-15T05:32:57.446-07:00IBLabookInternal web-based resource for <span class="blsp-spelling-error" id="SPELLING_ERROR_0">IBL</span> people can be accessed here: <a href="http://iblabook.blogspot.com/search/label/1%29%20Lab%20Meeting"><span class="blsp-spelling-error" id="SPELLING_ERROR_1">IBLabook</span></a>. If you have problems <span class="blsp-spelling-corrected" id="SPELLING_ERROR_2">accessing</span> it, think you <span class="blsp-spelling-corrected" id="SPELLING_ERROR_3">should</span> be given access, or have <span class="blsp-spelling-corrected" id="SPELLING_ERROR_4">recommendations</span> for changes to what is available there please bring it up at the weekly lab meeting, <span class="blsp-spelling-corrected" id="SPELLING_ERROR_5">Tuesday's</span> 9am at <span class="blsp-spelling-error" id="SPELLING_ERROR_6">HMB</span> 13.304.Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-30016212825943895932007-05-10T11:39:00.000-07:002007-05-10T11:50:02.824-07:00Integrative Bioinformatics 7XML mediated interoperability between data structures. <span style="color:#990000;"><strong>The basic idea is very simple: [environment/structure 1] --> XML --> [environment/structure 2]</strong></span>. A very powerful suite of tools, formal and computational, have been developed to deal with the mediation so we have plenty to keep you busy for a couple of hours.<br /><br />For the <span class="blsp-spelling-error" id="SPELLING_ERROR_0">Matlab</span> centric exercises please note the <span class="blsp-spelling-error" id="SPELLING_ERROR_1">xmlread</span>, <span class="blsp-spelling-error" id="SPELLING_ERROR_2">xmlwrite</span> and <span class="blsp-spelling-error" id="SPELLING_ERROR_3">xslt</span> commends. Have a go at the <a href="http://www.w3.org/">W3C</a> links listed in the help files of those commands. In <span class="blsp-spelling-corrected" id="SPELLING_ERROR_4">today's</span> class we are going to cheat and use tools that both rely on <span class="blsp-spelling-error" id="SPELLING_ERROR_5">Matlab</span> structures and/or can <span class="blsp-spelling-corrected" id="SPELLING_ERROR_6">manipulate</span> them using <span class="blsp-spelling-error" id="SPELLING_ERROR_7">XPath</span>. I'll also explain why this is a very popular and useful cheat in any language. Note also that the best libraries are often produced by people with <span class="blsp-spelling-corrected" id="SPELLING_ERROR_8">the</span> same problems as you. For example see these two: <a href="http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=4278&objectType=file">XML Toolbox</a> and <a href="http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=1757&objectType=file">XML Parser</a>. I also wrote a <span class="blsp-spelling-corrected" id="SPELLING_ERROR_9">library</span> to deal with XML mediation <a href="http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=6268&objectType=FILE">XML4MAT</a> but one of you (no names please) told me it is ugly.Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com1tag:blogger.com,1999:blog-5169185715228913187.post-53471425969847111432007-05-03T10:42:00.000-07:002007-05-03T10:55:01.536-07:00Integrative Bioinformatics 6<span style="font-size:130%;color:#006600;"><strong>Modelling Strings</strong></span><br /><br /><span style="font-family:verdana;color:#000099;">Today we have a hands on tutorial on modelling strings and how you can use them to represent and/or retrieve structured information. This will be a class on menial Bioinformatics.</span><br /><span style="font-family:Verdana;color:#000099;"></span><br /><span style="font-family:Verdana;color:#000099;">Modelling strings relies heavily on <a href="http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/access/helpdesk/help/techdoc/matlab_prog/f0-42649.html&http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_prog/f0-42649.html#bqxyt6c-4">regular expressions</a>. Spend some time getting familiar with the concepts of patterning, lazy and greedy quantifiers and tokens. Try the <em>regexp</em> function with all 5 output arguments to see what is there.</span>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-25712565112178712322007-04-25T14:19:00.000-07:002007-04-25T14:38:00.865-07:00Integrative Bioinformatics 5<span style="font-size:130%;color:#006600;"><strong>Case Study: Ovary Cancer data integration at the Kleberg Foundation</strong></span><br /><br /><span style="color:#ff0000;">NOTE THE LOCATION FOR THIS CLASS IS IN THE SOUTH CAMPUS</span><br /><span style="color:#ff0000;">(SCRB1. conference room 4) </span><br /><p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a>]<br /><br /><span style="color:#000099;">Lets get serious: you now have data structures that describe your (or at least Katherine's) data so the time has come to show you how it all fits together. Instead of having the class in HMB this time you are invited to join a workshop about this topic in the South Campus. We'll do two things:</span></p><p><span style="color:#000099;">1. I'll post a sample solution of a script that would assemble a data structure for K's data. The idea is not that my solution is the best, it is just to encourage you to post your own m-files assembling alternative data structures. This way next week we'll be generating multiple XML structures from the different solutions.</span></p><p><span style="color:#000099;">2. You are asked to listen to my short presentation at 2:10 pm encouraged to participate in the followup discussion. Here's the full agenda for the afternoon in case you can and want to hear the full story:</span></p><p><span style="color:#660000;">Workshop at the Kleberg Center for Biomarker discovery,South Campus Research Building (SCRB1. conference room 4) behind the welcome desk to the right upon entering the building.<br />01:15 pm -01:30 pm<br />Dr. Rahul Mitra – Kleberg Center<br />Introduction</span></p><p><span style="color:#660000;">01:35 pm - 02:05 pm<br />Dr. Bryan Hennessy – Kleberg Center<br />Molecular Medicine Studies on ovarian and breast cancers at Kleberg Center</span></p><p><span style="color:#990000;">02:10 pm - 02:40 pm<br />Dr. Jonas Almeida – Kleberg Center<br />Data collection and analysis at Kleberg Center</span></p><p><span style="color:#990000;">02:45 pm - 03:45 pm<br />All: Open discussion</span></p><p><br /></p>Jonas Almeidahttp://www.blogger.com/profile/09423932476255402491noreply@blogger.com0tag:blogger.com,1999:blog-5169185715228913187.post-30440126400630341392007-04-18T09:01:00.000-07:002007-04-25T14:34:44.052-07:00Integrative Bioinformatics 4XML constructs<br /><br /><p>[<a title="Index of classes" href="http://integrativebioinformatics.blogspot.com/2007/03/integrative-bioinformatics-integrative.html">Index of classes</a>] <span style="color:#660000;"><br /><br />What is XML?<br />In this class we are going to learn what are the main features of XML, and how it can be used to build data structures (including some insights on the homework ;-) ). XML is one of the most popular and widely used representation languages on the web. Since it's implementation in 1996 (originally by the SGML Editorial Review Board), it has been widely extended and became a w3c recommentation in 2006. Due to it's flexibility many standard development teams in biomedical research have relied on XML to implement knowledge domain representations, such as MAGE-ML, MiniML, SBML, AGML, etc.<br />On a different line of though, we are also going to learn how to use S3DB through the API, by building (surprisingly!!) an XML structure that resembles SQL.<br /><br />For more on XML visit <a href="http://www.w3.org/XML/">the W3C recommendation</a> and <a href="http://www.w3schools.com/xml/">the tutorial</a>.</p></span><br /><span style="color:#660000;"></span>Unknownnoreply@blogger.com0