tag:blogger.com,1999:blog-3218932645625415604Thu, 17 May 2012 12:31:31 +0000BioHDFChIP-SeqSOLiDmiRNAP4 medicineCancerFundingGeneSifterFirecrestStandardsDNA sequencingVolunteerMicroarrayfinderOpen-SourceSaaSIon TorrentSystems biologyGeospizaGeraldDNA sequence qualityiFinchBigDataIllumina GANext Generation SequencingRNA-seqFinchTVGenetic AnalysisMaqFinchLabBest Practice GuidesLIMS454Tag ProfilingCloud Computingsmall RNABustardHDF5PacBioWorkflowHelicosdatabasesVariation AnalysisWhole Transcriptome AnalysisABRFSolexaFinch SuiteWeb resourcesTranslational BioinformaticsCore LabAGBTResequencingGeneSifter Lab EditionGeneSifter Analysis Editionbioinformatics teachingBioinformaticsLike our namesake, Geospiza is continually evolving. Follow the conversation to learn how you can make the most of your data.http://finchtalk.geospiza.com/noreply@blogger.com (Sandra Porter)Blogger147125tag:blogger.com,1999:blog-3218932645625415604.post-7239645729444167500Tue, 08 May 2012 16:30:00 +00002012-05-17T05:30:34.974-07:00FinchTV Okay, it took a while, but FinchTV, Geospiza's popular Sanger sequencing trace viewer is now available on Mac OS X Lion. While the same great features are still great, the underlying code has been updated to run the application as a native intel binary, so it can be great into the future. Features make FinchTV cool In addition to all the basic things you'd expect a trace viewer to do like http://finchtalk.geospiza.com/2012/05/finchtv-on-lion.htmlnoreply@blogger.com (Todd Smith)2tag:blogger.com,1999:blog-3218932645625415604.post-7172554351546208990Sun, 22 Apr 2012 14:59:00 +00002012-04-22T08:00:42.005-07:00GeneSifter Analysis EditionNext Generation SequencingBioinformatics Join us Thursday, May 3, 2012 9:00 am (Pacific Time) for a webinar on analyzing DNA sequencing data with hundreds of thousands to millions of nucleotide variants. Description: This webinar discusses DNA variant detection using Next Generation Sequencing for targeted and exome resequencing applications as well as, whole transcriptome sequencing. The presentation includes an overview of each http://finchtalk.geospiza.com/2012/04/sneak-peak-practical-approach-to.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-9161297390955300559Fri, 02 Mar 2012 18:49:00 +00002012-03-02T10:49:06.094-08:00Come find out at our two Seattle seminars on March 6 and March 13. In these seminars we will show you how you can get answers to your RNA-Seq and Exome Analysis questions. From the brochure: Learn how GeneSifter® Analysis Edition helps you manage the bioinformatics workload, so you can focus on scientific discovery. GeneSifter combines comprehensive data analysis with meaningful visualization http://finchtalk.geospiza.com/2012/03/you-have-500-million-reads-now-what.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-2269631694805430742Tue, 14 Feb 2012 23:08:00 +00002012-02-14T15:08:00.733-08:00AGBTDNA sequencingBioinformaticsThe annual Advances in Genome Biology and Technology (AGBT) begins tomorrow and would not be complete without a couple of contributions by @finchtalk. Follow the tweets at #AGBT and if you are at the conference visit posters 334 and 335 (abstracts below). Also, visit Lanai 189 to see the latest advances in genome technology and software from the Caliper and Geospiza organizations within http://finchtalk.geospiza.com/2012/02/sneak-peak-poster-presentations-at-agbt.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-763920350490074116Tue, 24 Jan 2012 17:55:00 +00002012-02-16T06:19:43.850-08:00GeneSifter Analysis EditionDNA sequencingGeneSifter Lab EditionCloud ComputingBioinformaticshttp://finchtalk.geospiza.com/2012/01/sneak-peak-cost-effective-sequencing-by.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-6452731732070016672Thu, 05 Jan 2012 15:53:00 +00002012-01-06T18:08:01.047-08:00databasesBioinformatics Let's get 2012 started with an update on the growth of biological databases.  About this time last year, I summarized Nucleic Acids Research's (NAR) annual database issue where authors submit papers describing updates to existing databases and present new databases. In that post, I predicted that we would see between 60 and 120 new databases in 2011.  This year's update included 92 new http://finchtalk.geospiza.com/2012/01/bio-databases-2012.htmlnoreply@blogger.com (Todd Smith)2tag:blogger.com,1999:blog-3218932645625415604.post-168934329350447358Wed, 09 Nov 2011 03:37:00 +00002011-11-08T19:38:29.885-08:00HDF5BigDataNext Generation SequencingCloud Computing Next week, Nov 12-18, Super Computing comes to Seattle. On Wed, Nov 15 at 12:15-1:15 pm, @finchtalk (me) will host a Birds-of-a-Feater session on "Technologies for Managing BioData" in room TCC305. I'll kick off the session by sharing stories from Geospiza's work experiences and the work of others. If you have a story to share please bring it. The session will provide an open platform. We planhttp://finchtalk.geospiza.com/2011/11/biodata-at-sc11.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-6333760728456761382Thu, 13 Oct 2011 12:54:00 +00002011-10-13T05:54:45.086-07:00ResequencingGenetic AnalysisP4 medicineNext Generation Sequencing "People say they want their genetic information, but they don’t." "The speaker's views of data return are frankly repugnant." These were some of the [paraphrased] comments and tweets expressed during Cold Spring Harbor's fourth annual conference entitled "Personal Genomes" held Sep 30 - Oct 2, 2011. The focus of which was to explore the latest technologies and approaches for sequencing http://finchtalk.geospiza.com/2011/10/personalities-of-personal-genomes.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-7350833958795409089Fri, 30 Sep 2011 23:50:00 +00002012-02-16T06:20:12.040-08:00http://finchtalk.geospiza.com/2011/09/sneak-peak-using-ngs-to-identify-tumor.htmlnoreply@blogger.com (Todd Smith)1tag:blogger.com,1999:blog-3218932645625415604.post-843711481210826077Wed, 10 Aug 2011 23:15:00 +00002011-08-11T15:41:30.304-07:00Systems biology Stitch-Seq, one of the newest editions to the Next Generation DNA Sequencing (NGS) was presented in June's Nature Methods. Back in 2008, when groups were realizing the power of NGS technologies, I entitled a post "Next Gen Sequencing is not Sequencing DNA" to make the point that massively parallel ultra-high throughput DNA sequencing could be used to for quantitative assays that can measure http://finchtalk.geospiza.com/2011/08/stitching-protein-protien-interactions.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-5010925466055102659Fri, 08 Jul 2011 23:46:00 +00002011-07-08T16:46:28.074-07:00GeospizaVolunteerPerkinElmer is committed to improving human and environmental health. Sometimes that extends beyond delivering commercial products and services to how we participate in our community. Geospiza was proud to help the local community last Tuesday (7/5) by volunteering, through PerkinElmer's Corporate Social Responsibility program, to clean up the area around Lake Union after the Seattle's Fourth http://finchtalk.geospiza.com/2011/07/its-not-just-science-and-technology.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-8442661350431475350Fri, 10 Jun 2011 14:29:00 +00002011-06-10T07:29:11.364-07:00GeneSifter Analysis EditionGenetic AnalysisNext Generation SequencingBioinformaticsJoin us next Wed. June 15 for a webinar on resequencing applications. Description: This webinar will focus on DNA variant detection using Next Generation Sequencing for the applications of targeted and exome resequencing as well as, whole transcriptome sequencing. The presentation will include an overview of each application and its specific data analysis needs and challenges. Topics covered http://finchtalk.geospiza.com/2011/06/sneak-peak-ngs-resequencing.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-6885362879326783749Tue, 07 Jun 2011 20:58:00 +00002011-06-07T14:01:17.640-07:00PacBioIon Torrentbioinformatics teachingIllumina GASOLiDNext Generation Sequencing Cactus at Bandelier National Monument  Last week, June 1-3, the Department of Energy held their annual Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico.  SFAF, also sponsored b the Joint Genome Institute, and Los Alamos National Laboratory and was attended by individuals from the major genome centers, commercial organizations, and smaller labs. In addition http://finchtalk.geospiza.com/2011/06/does-2011-sequencing-finishing-analysis.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-4623035507897111001Fri, 20 May 2011 20:31:00 +00002011-05-20T13:31:57.571-07:00Systems biologyP4 medicineLast Sunday and Monday (5/15, 5/16/11) the Institute for Systems Biology (ISB) held their annual symposium. This year was the 10th annual and focused on "Systems Biology and P4 Medicine." For those new to P4 medicine, the Ps stand for Personalized, Predictive, Preventative, and Participatory. P4 medicine is about changing our current disease oriented, reactive, approaches to those that prevent http://finchtalk.geospiza.com/2011/05/21st-century-medicine-question-of-ps.htmlnoreply@blogger.com (Todd Smith)2tag:blogger.com,1999:blog-3218932645625415604.post-316691323012378285Fri, 06 May 2011 14:57:00 +00002011-05-06T07:57:48.428-07:00Yesterday, May 5th, PerkinElmer announced that they have acquired Geospiza. This is exciting news and a great opportunity for Geospiza's current customers, future clients, and the company itself. From numerous tweets, to more formal news coverage, the response has been great. Xconomy, Genome Web, Genetic Engineering & Biotechnology News (GEN), and many others have covered the story and http://finchtalk.geospiza.com/2011/05/big-news-perkinelmer-acquires-geospiza.htmlnoreply@blogger.com (Todd Smith)1tag:blogger.com,1999:blog-3218932645625415604.post-8476604817448883355Thu, 28 Apr 2011 22:07:00 +00002011-04-28T15:07:22.109-07:00GeneSifter Analysis EditionGeneSifterGeneSifter Lab EditionSpring is here and so are new releases of the GeneSifter products. GeneSifter Lab Edition (GSLE) has been bumped up to 3.17 and GeneSifter Analysis Edition (GSAE) is now at 3.7. What's New? GSLE - This release includes big features along and a host of improvements. For starters, we added comprehensive inventory tracking. Now, when you configure forms to track your laboratory processes, you can http://finchtalk.geospiza.com/2011/04/product-updates-genesifter-lab-and.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-7004008072890635450Thu, 21 Apr 2011 21:46:00 +00002011-04-21T14:46:11.951-07:00 What do science, culture, and policy have in common? In order to improve the quality and affordability of health care, all three have to change. This message is central to Sage Bionetworks’ mission and the theme from this year’s Sage Commons Congress held April 15th and 16th in San Francisco. What’s the problem?  Biology is complex. This complexity makes it difficult to understand why some http://finchtalk.geospiza.com/2011/04/science-culture-policy.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-5665485624167293393Wed, 06 Apr 2011 13:51:00 +00002011-04-06T06:53:20.692-07:00small RNAGenetic AnalysisGeneSifterTranslational BioinformaticsTag ProfilingRNA-seqBioinformaticsJoin us next Tuesday, April 12 at 10:00 am PST for a webinar focused on RNA-Seq applications in breast cancer research. The field of cancer genomics is advancing quickly. News reports from the annual American Association of Cancer Research meeting are indicating that whole genome sequencing studies such as the 50 breast cancer genomes (WashU) are providing more clues about the genes that may be http://finchtalk.geospiza.com/2011/04/sneak-peak-rna-sequencing-applications.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-4048158341868698355Wed, 23 Mar 2011 14:32:00 +00002011-03-23T07:58:23.619-07:00Translational BioinformaticsDuring the week of March 7, I had the pleasure of attending the AMIA’s (American Medical Informatics Association) summit on Translational Bioinformatics (TBI), at the Parc 55 Hotel in San Francisco. What is Translational Bioinformatics?  Translational Bioinformatics can be simply defined as computer related activities designed to extract clinically actionable information from very large http://finchtalk.geospiza.com/2011/03/translational-bioinformatics.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-6042160448224215459Thu, 10 Mar 2011 23:03:00 +00002011-03-22T16:07:07.093-07:00GeneSifterRNA-seqBioinformaticsNext week (March 14-18, 2011) is CHI's X-Gen Congress & Expo. I'll be there presenting a poster on the next challenge in bioinformatics, also known as the information bottleneck. You can follow the tweet by tweet action via @finchtalk or #XGenCongress. In the meantime, enjoy the poster abstract. The next generation challenge: developing clinical insights through data integration Next http://finchtalk.geospiza.com/2011/03/sneak-peak-next-generation-challenge.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-7096404077799571917Thu, 03 Mar 2011 18:37:00 +00002011-03-03T10:40:51.502-08:00In Blink, Malcolm Gladwell discusses how experts do expert things. Essentially they develop granular languages to describe the characteristics of items, or experiences. Food tasters, for example, use a large and rich vocabulary with scores to describe a food’s aroma, texture, color, taste, and other attributes. We characterize DNA variation in a similar way In a previous post, I presented a http://finchtalk.geospiza.com/2011/03/flavors-of-snps.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-5240740482951216310Wed, 02 Mar 2011 01:16:00 +00002011-03-02T12:16:29.135-08:00Join us next Tuesday, March 8 at 10:00 am Pacific Time for a webinar on Next Gen sequence data analysis. Register Today! http://geospizaevents.webex.com Please note the previous post had Wed. listed for the day. The correct day is Tue.http://finchtalk.geospiza.com/2011/03/data-analysis-for-next-generation.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-7587097573611515393Wed, 16 Feb 2011 14:20:00 +00002011-02-16T06:20:40.797-08:00GeneSifterDNA sequencingABRFThe Association for Biomedical Research Facilities conference begins this weekend (2/19) with workshops on Saturday and sessions Sunday through Tuesday.  This year's theme is: Technologies to Enable Personalized Medicine, and appropriately a team from Geospiza will be there at our booth and participating in scientific sessions.  I will be presenting a poster entitled, "Clinical Systems for Cancerhttp://finchtalk.geospiza.com/2011/02/sneak-peak-abrf-and-software-systems.htmlnoreply@blogger.com (Todd Smith)1tag:blogger.com,1999:blog-3218932645625415604.post-3830900747094746989Fri, 11 Feb 2011 19:03:00 +00002011-02-12T12:36:29.091-08:00GeneSifterNext Generation SequencingGeneSifter Lab EditionBioinformaticsYesterday and two weeks ago, Geospiza released two important news items.  The first announced PerkinElmer's section of the GeneSifter® Lab and Analysis systems to support their new DNA sequencing service. The second was an announcement of our new SBIR award to improve variant detection software. Why are these important? The PerkinElmer news is another validation of the fact that software http://finchtalk.geospiza.com/2011/02/variant-analysis-and-sequencing-labs.htmlnoreply@blogger.com (Todd Smith)0tag:blogger.com,1999:blog-3218932645625415604.post-1275797033466408946Tue, 08 Feb 2011 22:30:00 +00002011-02-16T06:08:31.053-08:00AGBTDNA sequencingBioinformaticsMore. That's how I describe this year's conference. More attendees More data More genomes More instruments More tweeters More tweeting controversy More software More ... Feel free to add more comments.http://finchtalk.geospiza.com/2011/02/agbt-2011.htmlnoreply@blogger.com (Todd Smith)0