Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Recently I had shared a piece of news on the same topic:-  https://www.linkedin.com/feed/update/urn:li:activity:6590633791084163072/ # lims hashtag # laboratories hashtag # datamanagement hashtag # flexible Data Management Challenges In Next Generation Sequencing Since the beginning of the Human Genome Project, data management has been perceived as a key challenge for current molecular biology research. Before the finish of the nineties, advances had been set up that adequately bolstered most continuous activities, ordinarily based upon relational database management frameworks. Ongoing years have seen a sensational increment in the amount of information created by running projects that extends in this area. While it took over ten years, roughly three billion USD, and in excess of 200 gatherings worldwide to collect the main human genome, the present sequencing machines create a similar amount of crude information in seven days, at an expense of around 2000 USD...

3 Days National Level Workshop on "NGS Data Analysis:Variant Calling,RNASEQ,CHIPSEQ"' 8th to 10th March 2019 09:30 AM - 05:00 PM Topics Covered ▪ Introduction to Bioinformatics ▪ Data curation using Biological databases ▪ Understanding the concept of Gene Expression & Genome Editing ▪ Gene Finding Tools ▪ Introduction to Next Generation Sequencing ▪ Searching for SRA Data for genomic samples ▪ Introduction to Sequence alignment, BLAST ▪ Variant Calling to detect mutations ▪ RNA sample studies for gene expression ▪ Introduction to ChIP-Seq technology Our 3 days comprehensive Workshop on Next Generation Sequencing Data Analysis,Variant Calling, RNAseq, ChIPseq : A Practical Introduction aims at providing systematic Hands-on-Training on using Data Analysis application/tools for the NGS data. This workshop had been conceptualized by eminent scientist having substantial experience in the field of Data Analysis. ...

Established in 2011, Bionivid Technology, located in the happening start-up hub of Bangalore, is a genomics and informatics start-up, jointly cofounded by Mr Madavan Vasudevan, Mr Rohit Nandan Shukla and Mr Hitesh Goswami. Mr Madavan is a qualified microbiologist-turned-bioinformatician; His partner Mr Rohit is also a qualified bioinformatician and a certified programmer; and Mr Hitesh is a neurobiologist with a fine business acumen. All three of them make a perfect ingredient for raising a hot bioinformatics start-up. - See more at: http://www.biospectrumindia.com/biospecindia/features/221910/hot-start-ups-believe-leap-faith#.dpuf

Qiagen has purchased the assets of Biobase, a Wolfenbüttel, Germany-based provider of curated biological databases, for an undisclosed sum. Qiagen said that Biobase will be renamed Qiagen Wolfenbüttel. Also, Michael Tysiak, BioBase's CEO, will join Qiagen as general manager of the newly purchased company. Founded in 2007, Biobase provides access to curated data assembled by subject matter experts and organized in an accessible and easy to search manner. Its databases support projects focused on functional and gene regulation analyses, variant annotation, pharmacogenetics-based analysis, and more. Among its repositories are the Human Gene Mutation Database (HGMD), which offers access to information on inherited disease mutations; GenomeTrac, which contains data on pathogenic variants; the PharmacoGenomic Mutation Database, which serves as a resource for locating variants that affect drug response; and the Transcription Factor Binding Sites database, which contains information o...

This is really getting interesting, BioSaga is making history as we keep blogging! The  GATTACA SAGA ! is coming to an reality! The Race has just begun! today for  Olympian Genes; tomorrow may be for a pianist with pair of hands with 6 fingers each!  There is now no limt to the human imagination there could be a new profession  as GENE ARCHITECT or a GENOME SCULPTOR!  Beginning in 2015, Uzbekistan says it will incorporate genetic testing into its search for Olympic athletes, the Atlantic reports. Rustam Muhamedov from Uzbekistan's Institute of Bioorganic Chemistry's genetics laboratory notes that he and his colleagues have been studying the genes of Uzbek athletes and are working on developing a set of 50 genes to determine what sport a child is best suited for. "Developed countries throughout the world like the United States, China, and European countries are researching the human genome and have discovered genes that define a...

O ne more story in our very own GATTACA SAGA ! Patient advocacy groups Global Genes and Swan USA announced on Tuesday a program to provide whole-exome sequencing to patients with rare diseases who cannot afford such services. Beginning March 1, Global Genes and Swan USA will provide funding for the whole-exome sequencing of about 30 undiagnosed patients in order to identify the genetic bases of their ailments. Parabase Genomics and the UCLA Clinical Genomics Center were selected as the first clinical genomic sequencing providers for the pilot project. Global Genes is a rare and genetic disease patient advocacy group, and Swan USA provides support to families of children living with diseases and syndromes that have yet to be named. According to them, a genomic test costs between $3,500 and $5,000. The financing for the program was raised through a donor-directed fund launched in September, and additional funding is underway in order to expand the program to include more undia...

Here are some bioinformatics courses, These are geared towards: - Scientists, so they can think like a programmer and solve bottlenecks in data-based Biology - Computer programmers, so they know how to solve bioinformatics problems for scientists - Bioinformaticians, so they can advance their skills in newer application areas Some of these courses include scripting and database management with Linux, Perl, R, Matlab and MySql, while others include learning to use software for analyzing data from Microarray, NGS, Metabolomics and Proteomics platforms. A course on High Performance Computing and Primer Design is also offered. A detailed roster of scheduled courses is available at: http://www.bioinformatics.org/edu/calendar/view.php?view=upcoming Additionally, through Bioinformatics.org, an instructor-led program in practical bioinformatics is being offered. The goal here is to provide attendees a broad overview of the bioinformatics landscape, while giving them hands-on experienc...

GATTACA has always been one of my favorites; every now and then I have used it as a reference in many of my posts, this one being the recent! Genome From Birth - Dawn of the GATTACA era! This is what Senator Rand Paul (R-Ky.) says in his latest public address; Speaking at a Liberty University event in Virginia, Senator Rand Paul (R-Ky.) warned that genetic testing could lead to eugenics à la the 1997 movie Gattaca , reports the Associated Press . "In your lifetime, much of your potential — or lack thereof — can be known simply by swabbing the inside of your cheek," Paul said. "Are we prepared to select out the imperfect among us?" He was campaigning in Virginia for gubernatorial candidate Ken Cuccinelli. Other aspects of Paul's speech referring to the dystopian movie, though, resembled the Wikipedia entry on the movie, Rachel Maddow pointed out on her show on Monday. USA Today notes that Paul has not responded to those accusations. Paul added tha...

Illumina today announced it signed a definitive agreement to acquire clinical software firm NextBio. NextBio, based in Santa Clara, Calif., provides platforms to aggregate and analyze large amounts of phenotypic and genomic data for research and clinical applications. It currently has customers at more than 50 commercial entities and academic institutions. By acquiring the firm, Illumina "will be able to offer customers enterprise-level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare," according to a company statement. NextBio's platform allows customers to compare experimental data against existing data sets using a correlation engine, enabling them to discover new associations. It uses "highly scalable" software-as-a-service enterprise technology and is capable of analyzing petabytes of data. Illumina plans ...

Qiagen has acquired CLC Bio, a privately held bioinformatics software company headquartered in Aarhus, Denmark. The news was first reported on AllSeq's blog . This is the second bioinformatics company that Qiagen has purchased this year. In May, it bought Ingenuity Systems for $105 million in cash to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions ( BI 5/3/2013 ). Qiagen has been making some interesting moves lately, slowly building an end to end sequencing solution. They’ve already established themselves as the market leaders in sample prep, but then they started acquiring the missing pieces. First they bought Intelligent BioSystems in June 2012, giving them access to a sequencing platform built with the clinical market in mind (fairly standard SBS chemistry, relatively fast runs and multiple flow cells to obviate the need for sample multiplexing). Then they ...

Following Roche's disclosure last week that it will shut down 454 Life Sciences and stop supporting 454 sequencing instruments by 2016, customers are making plans to move their sequencing over to other platforms, if they have not done so already. While Illumina, Life Tech's Ion Torrent, and Pacific Biosciences are eager to step in to fill the void, some customers say aspects of 454's technology cannot be replaced by other platforms at this point. Also, those customers who have started to use 454 for routine clinical applications need to revalidate their assays on a new platform. Roche said last week that it will close down 454, which is based in Branford, Conn., and lay off about 100 employees over the next three years ( GWDN 10/15/2013 ). By mid-2016, it will stop supporting the 454 sequencing platforms, the GS FLX+ and the GS Junior. Roche's decision to pull the plug on 454 came to light less than a month after the company announced a deal with Pacific Bios...

Dawn of the GATTACA era! this was one of my old post. AND now this is what we hear from Robert Green The idea of sequencing someone's genome at birth has been "has been around for a long time in a pie-in-the-sky way," Robert Green from Brigham and Women’s Hospital tells Carl Zimmer at Slate . But it is becoming more of a reality, Zimmer adds. Green's BabySeq project recently received funding from the US National Institutes of Health to study how sequencing the genomes of some 240 healthy and ill infants affects their lives. They will be compared to a similar cohort of infants whose genomes will not be sequenced. As the study is small, Zimmer notes that rare, deleterious mutations may not crop up. The project will, though, make the discussion of ethics in genomic medicine more concrete, he says. “We’ll be grappling with them in real life, with real babies and real families and real clinicians and real laboratory results,” Green adds.

                      -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-                         BI231 NGS Data Analysis                             June 24-28, 2013                       Online at Bioinformatics.Org          http://www.bioinformatics.org/wiki/BI231_NGS_Data_Analysis                    http://www.bioinformatics.org/edu/AGGT -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics to be covered include the description of sequencing strategies and platforms, experiment types, data format...

Qiagen said this week that it acquired Ingenuity Systems for $105 million in cash in order to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions — from sample preparation to data interpretation. Under its new parent, Ingenuity will continue to operate out of its offices in Redwood City, Calif., and retain all 120 current employees, while CEO Jake Leschly takes on new responsibilities within Qiagen's life science business unit. Ingenuity will also continue to develop and offer products under its existing licensing scheme. Its portfolio includes a knowledgebase of curated genomic variants; Ingenuity Pathway Analysis, its web-based application for modeling and analyzing biological pathways; Ingenuity Variant Analysis, which selects clinically relevant genomic variants from NGS data ( BI 1/13/2012 ); and Ingenuity iReport, its software for reporting the results of gene ...

BGI-Shenzhen today said that it has extended its offer to acquire Complete Genomics for around $118 million until midnight New York City time on Dec. 14. BGI's tender offer to acquire all of the shares of Complete Genomics was previously scheduled to expire today. As of the close of business last night approximately 15.4 million shares of Complete Genomics' common stock, or 44 percent of its outstanding shares, were tendered and not withdrawn. The extension of the offer last night coincided with a letter Illumina sent to Complete Genomics' board of directors urging them to reconsider Illumina's offer to acquire the firm for around $123 million. Earlier this week Illumina confirmed that it had made an unsolicited offer of $3.30 per share to acquire Complete Genomics. That offer is 5 percent higher than the price agreed between BGI and Complete Genomics. Complete Genomics turned down Illumina's offer saying that it would likely be turned down by regulator...

This is getting interesting every day! I love this Idea! sell a company but before selling it split or spin off as another company with a future technology (Illumina). After a few years again sell or get acquired! Citing vast future potential, ISS has sided with Illumina in the gene-sequencing company’s fight to hold off a hostile bid from Roche Holding. The proxy advisor says shareholders should vote the Illumina board back into service, and reject Roche’s slate because the offer probably undervalues the future of Illumina. Roche  last week raised its offer for Illumina to $51 a share from $44.50 , and called it fair and full. But Illumina shares immediately went above $51, and some in the market have pointed to $60 as the number to get the deal done. Illumina rejected the offer,  citing a report that compared the company to Apple and Illumina’s products to iPads.  The company has argued that Roche’s bid came just after Illumina’s own shares had cratered on a ba...