Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Effective data management is a crucial piece of deploying the IT systems that run lab applications and provide analytical information to help drive scientific and operational decision-making and strategic planning by executives, managers, and end-users. Register for this webinar   https://www.linkedin.com/posts/kameshwaran_labcast-session-effective-ways-of-managing-activity-6676769940088856576-e9Vh

At the Bio-IT World Conference last week, Intel unveiled a new website, dubbed Optimized Code, that offers access to versions of several popular open-source bioinformatics analysis tools that the company has optimized to run on Intel Xeon processors, with the aim of generating results faster and more efficiently than standard iterations of these solutions. The first set of applications that the company has released specifically for genomic analysis include optimized versions of  the Broad Institute's Genome Analysis Toolkit ; Blast algorithms for nucleotide- and protein-based sequence searching; BWA-ALN , software for mapping low-divergent sequences to a reference genome; and MPI-HMMER , protein sequence analysis software. The company has also released optimized code for AMBER and NAMD, both of which are used for simulating the molecular dynamics of biomolecular systems. The Intel website provides performance numbers for each of the optimized codes as well as directions for h...

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 ...

Courtesy Xconomy After merging with Symyx Technologies in 2010, acquiring Contur Sofware in 2011, and buying VelQuest earlier this year, San Diego scientific software developer Accelrys says today it is buying Aegis Analytical. Accelrys is paying $30 million in cash for Aegis, a company based in Lafayette, CO, (near Boulder) that makes software used to monitor biotech product development and manufacturing processes. In a  statement  today, Accelrys says the deal helps to further expand its suite of software used to manage the life cycle of innovation among pharmaceutical companies and in other industries. Aegis has about 40 full-time and contract employees, and “the idea is to keep the business in Boulder and fairly intact,” Accelrys CFO Michael Piraino told me during a phone interview earlier this afternoon. Aegis CEO Robert Di Scipio will stay with the merged company through the transition to new ownership. About two-thirds of Acce...

wwwtilda Data manager in computational material science Introduction Tilde (wwwtilda, ~) is a data manager in cheminformatics and computational material science. The nowadays situation in these disciplines with a plenty of incompatible data formats is rather confusing. Furthermore a new approach to the scientific data verification and exchange is desired because the traditional peer-reviewed journals and their supplementary materials sections do not solve this task properly. Therefore Tilde aims to simplify data processing and exchanging for the scientists, dealing with popular computer simulation packages in material science (e.g.  VASP ,  CRYSTAL ,  WIEN2K  etc). Now the text outputs of these programs can be collected, and the calculated results therein can be visualized. The example focus is on phonon properties of the crystalline materials: vibrational spectra, band structures, densities of states, vibrational patterns visualization etc. Moreover Ti...

Elsevier, a world-leading provider of scientific, technical, and medical information products and services, announced today the acquisition of the business assets of  Ariadne Genomics , a provider of pathway analysis tools and semantic technologies for life science researchers. Ariadne will be integrated with Elsevier's Corporate Markets division. "Ariadne Genomics' pathway analysis tools and semantic technologies integrate research findings from across multiple content sources providing a deeper understanding of biological pathways and disease progression. Ariadne's products improve research productivity and outcomes for life science researchers by delivering new insights for potential interventions, therapies and cures," said Alexander van Boetzelaer, Managing Director of Elsevier Corporate Markets. "Ariadne brings to Elsevier an information offering in the biology domain and a passionate and dedicated team of life science professionals. Ariadne's team ...

For Indian laboratories, the decision to implement  informatics applications that support compliance with 21 CFR Part 11 delivers multiple benefits. They are protecting their access to regulated markets in the US and other countries while implementing electronic processes and procedures that can reduce costs while enhancing their ability to deliver world class results.

PerkinElmer reported after the close of the market on Thursday that revenues in the third quarter rose 8 percent year over year, but it missed analyst estimates on the top line. Total revenues in the quarter ended Oct. 2 rose to $453.7 million, compared to $419.1 million a year ago but fell short of Wall Street estimates of $469.6 million. On an organic basis, revenues were up 4 percent year over year. The firm has made a number of purchases throughout 2011 and in the quarter those acquisitions contributed more than $20 million to the top line, CFO Frank Wilson said on a conference call after the release of the company's earnings results. The Human Health segment grew revenues to $207.4 million, up 7 percent from $194.5 million a year ago, while Environmental Health climbed to $246.3 million, a 10 percent increase from $224.6 million a year ago. On the conference call, Chairman and CEO Robert Friel said that during the quarter, growth was seen across all major geographies and most ...

PerkinElmer, Inc., a global leader focused on the health and safety of people and the environment, today announced that it has signed a definitive agreement to acquire CambridgeSoft Corporation, and has completed the purchase of ArtusLabs, Inc.  These acquisitions will enhance the Company's focus on knowledge management in laboratory settings by expanding its informatics and software offerings, enabling customers to rapidly access and share enterprise-wide data for faster, more informed scientific decisions. The purchase of CambridgeSoft is expected to close in the second quarter, subject to customary closing conditions, including the expiration or termination of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act. Do you wish to know more?

The stats helper monkeys at WordPress.com mulled over how Bio Saga Blog did in 2010, and here’s a high level summary of its overall blog health: The  Blog-Health-o-Meter™  reads Fresher than ever. Crunchy numbers A helper monkey made this abstract painting, inspired by your stats. A Boeing 747-400 passenger jet can hold 416 passengers. This blog was viewed about  3,000  times in 2010. That’s about 7 full 747s. In 2010, there were  150  new posts, growing the total archive of this blog to 758 posts. The busiest day of the year was June 8th with 41  views. The most popular post that day was  Computational Biologist @ Pfizer UK . Where did they come from? The top referring sites in 2010 were  google.co.in ,  en.wordpress.com , emperan.com ,  obama-scandal-exposed.co.cc , and en.search.wordpress.com . Some visitors came searching, mostly for  list of pharma companies in noida ,  bioinformatics tools and softwares , ...

Belgian biotech firm Galapagos today announced its BioFocus service division has extended a contract with Amgen through 2012 to include target discovery and validation work. The extension will include the use of BioFocus' target discovery platform to deliver novel targets to support Amgen's therapeutic programs. Galapagos will receive €2 million ($2.6 million) in research fees in the first year, under the terms of the deal. It is also eligible for access fees and milestone payments. Originally forged in 2002, the collaboration between BioFocus, which Galapagos acquired in 2005, and Amgen involves identifying new molecules against drug targets. The partnership was extended in 2006 and 2008. BioFocus' discovery platform includes the use of  in vitro  and cell-based screening, structural biology, and chemogenomic and informatics tools.

In this article, in the first part, we propose an artificial neural network-based intelligent technique to determine the quantitative structure-activity relationship (QSAR) among known aldose reductase inhibitors (ARIs) for diabetes mellitus using two molecular descriptors, i.e., the electronegativity and molar volume of functional groups present in the main ARI lead structure. We have shown that the multilayer perceptron-based model is capable of determining the QSAR quite satisfactorily, with high  R -value. Usually, the design of potent ARIs requires the use of complex computer docking and quantum mechanical (QM) steps involving excessive time and human judgement. In the second part of this article, to reduce the design cycle of potent ARIs, we propose a novel ANN technique to eliminate the computer docking and QM steps, to predict the total score. The MLP-based QSAR models obtained in the first part are used to predict the potent ARIs, using the experimental data reported by Hu...

Linguamatics is currently seeking a talented post graduate with experience of natural language processing to work on leading edge text mining products. You will be responsible for developing and maintaining resources for domain specific adaptation of real-time semantic search software based on Natural Language Processing. Working closely with application scientists and the development team, you will ensure that the combination of software and resources satisfies customer requirements. This will include developing linguistic patterns, and programs to transform domain specific terminologies into common formats and keep them up-to-date. You will be working on life science applications, and some knowledge of the Pharmaceutical or Healthcare industry would be useful.In addition to resource and application development, you will be expected to contribute to ongoing UK or EU funded research projects as part of the research and resource development team. You will have strong communication ski...

Applications are invited for the post of Information Officer in Distributed Information Sub-Centre (DISC) established by Dept. of Biotechnology at Indian Institute of Advanced Research, Koba, Gandhinagar, Gujarat Applications are invited for the post of information officer at Distributed Information Sub-Centre (DISC) Position (scale), qualifications and experience: 1. Information Officer - one post Qualifications and Experience: M. Tech in IT sciences, MSc Bioinformatics with 2-3 years experience in the bioinformatics domain with expertise in database management, software development, system administration, and work experience on linux environment. Pay scale; Gross emoluments will be about Rs. 20.000/- pm in this post Application process: Please submit your application with biodata to Dr. DD Singh Bioinformatics Deptt. at  ddsingh@iiar.res.in  You can call at 079-30514150 for any queries. The application process is open till suitable candidate is found. Link...

Here is the climax of the stories  Life Technologies to Acquire Ion Torrent for up to $725M  and  The Argument Continues - Blue Ray or HD, Intel or AMD and now Illumina or Life Tech?   Life Technologies has completed its acquisition of Ion Torrent for $375 million in cash and stock.  The total value of the deal could rise by another $350 million if certain technical and time-based milestones are met through 2012. The acquisition adds Ion Torrent's semiconductor chip-based sequencing platform, which measures the release of hydrogen ions as nucleotides get incorporated by DNA polymerase. Unlike other existing second-generation sequencers, it does not require lasers, cameras, or labels.  The first system based on the technology is the Personal Genome Machine sequencer, which will be launched in the fourth quarter of this year. Life Technologies said that the transaction is expected to be $.02 dilutive to its earnings per share in 2010, neutral in 2011, and ac...

e-LICO multi-omics prediction challenge with background knowledge on Obstructive Nephropathy We present a biological data-mining problem that poses a number of significant challenges: The available data are of high dimensionality but of extre... Time Left:  90 days Teams:  84 Prize:  2500 EUR Share |

In a study appearing in the newest issue of the  Archives of Neurology , members of the Texas Alzheimer's Research Consortium reported that they have  identified protein biomarkers  in the blood that can be used to distinguish between individuals with and without Alzheimer's disease. The researchers compared protein patterns in blood samples from hundreds of individuals with or without Alzheimer's disease and incorporated these potential biomarkers into an algorithm for detecting Alzheimer's cases in a test group. Their results so far suggest this algorithm can accurately classify most Alzheimer's cases — particularly when combined with  APOE  status and demographic data. And, they said, information from the biomarker study is offering clues about possible sub-groups within Alzheimer's. For instance, by looking at some of the proteins that are frequently expressed at different levels in the blood of those with Alzheimer's disease, the team identified a pote...

Courtesy Bioclues The growing bioinformatics unit in the Cancer Research Center in Sheba medical center (Tel Hashomer) is looking for a PhD student and a bioinformatician (see attachments). The Cancer Research Center is equipped with state of the art technologies for high throughput data analysis, including Solexa sequencing machine. We also have the benefits of close access to clinical and diagnostics data. All making it a gold mine for bioinformaticans. The bioinformatics unit in the Sheba cancer research cancer is seeking for a bioinformatican. The projects involve programming and usage of advanced bioinformatics tools and include analysis of deep sequencing data. Contact:   eran.eyal@sheba.health.gov.il ,  972- 03-5308148 Share |

An account of  bioinformatics  education in India is presented   along with future prospects. Establishment of BTIS network by   Department of Biotechnology (DBT), Government of India in the   1980s had been a systematic effort in the development of  bioinformatics   infrastructure in India to provide services to scientific community.   Advances in the field of  bioinformatics  underpinned the need   for well-trained professionals with skills in information technology   and biotechnology. As a result, programmes for capacity building   in terms of human resource development were initiated. Educational   programmes gradually evolved from the organisation of short-term   workshops to the institution of formal diploma/degree programmes.   A case study of the Master’s degree course offered at   the  Bioinformatics  Centre, University of Pune is discussed.   Currently, many universities and in...