Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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...

Wow this an interesting article enjoy it! With the increasing ubiquity of smartphones, the growing popularity of tablets, and the burgeoning market for third-party applications, the public appetite for touchscreen technology is virtually impossible to ignore. It shouldn't, then, surprise anyone that bioinformatics software developers would look for ways to tap into the multi-touch market. But it's not just about making sure that download tallies are going up. In fact, some life science application developers say they dipped into the app space out of sheer curiosity more than anything else.   "For us, it was an experiment," says Andrew Su, an associate professor at the Scripps Research Institute. His laboratory developed an application called BioGPS, a mobile version of his group's web-based gene annotation portal, which runs on Apple's iPhone. "We imagined that somebody in a meeting or a seminar or at a conference who needed quick access to ...

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...

Genbios welcomes talented and committed people who wish to work alongside the best minds. If you hold a Ph.D or a Masters in Bioinformatics, Biotechnology, Microbiology, Software Engineering and Business Management, we invite you to be a part of the Genbios team. Please email your resume only to  info@genbios.in Current vacancies: Data curator and Analyst Qualification:  Graduate/ Post-graduate/ Diploma in Bioinformatics The job profile includes Literature survey Collection and curation biological data Bioinformatics analysis of data Database creation and management Skill set: Bioinformatics: A complete knowledge of the most commonly used bioinformatics databases and tools Information Science: Good knowledge in application of various programming languages such as Perl, Perl-CGI, Java, MySQL, PHP and related technologies for Bioinformatics. Experience in Linux environment is an advantage Life sciences: A very sound basic knowledge of biology is necessary. Good communicat...

Monsanto is a Fortune 500 Company, headquartered in St. Louis, Missouri. It has more than 20,000 employees at 320 locations worldwide in four primary regions – Europe/Africa, Asia Pacific, Latin America and North America. It has $11.7 billion in annual sales. In India, it started his operation in 1949 and is headquartered in Mumbai. Post : Application Support Specialist – Contract No of Post : Two Experience : 3 to 7 years Location : Bangalore Job Description : The successful candidate will become a member of Technology Pipeline Solutions (TPS) Team, part of Monsanto IT systems, supporting enterprise-level biotech and breeding related software applications. This is a very domain intensive role and will require deep understanding of various concepts in breeding, Biotechnology and data base applications. Job responsibilities : 1. Quick grasping of enterprise applications and their usage 2. Train the scientific community and ensure effective utilization of applications 3. Day to ...

Persistent Systems Ltd (PSL) has signed an agreement to acquire Agilent Technologies' software marketing and development business unit based in Grenoble, France. The acquisition is expected to be final by August 1, after which the unit will be called Persistent Systems, France. Dr Anand Deshpande, Chairman and Managing Director, PSL said the acquisition will contribute to Persistent's thrust in the life sciences and healthcare markets and also give it a presence in Europe. Around 30 domain experts from Agilent will come on board once the transaction is completed and more may be added, he said. The Agilent business is now focused on supplying data acquisition and control software for scientific instruments to the life sciences, environmental, energy, applied research and other markets. Currently, PSL's Life Sciences business contributes 10-12 per cent to its topline and was worth $20 million in FY 2011. The team here includes over 40 domain experts and more than 500 softw...

GeneGo today said that Agilent's GeneSpring bioinformatics solution has been integrated with GeneGo's MetaCore. The collaboration was announced in connection with the newest version of Agilent's GeneSpring. Agilent said today introduced GeneSpring GX 11.5, which can interpret microarray, proteomics, and metabolomics experiments together for the first time. The newest version includes a direct connection to the MetaCore pathway analysis engine, enabling users to seamlessly upload expression data analyzed in GeneSpring, said GeneGo. "MetaCore can concurrently visualize multiple types of data and will be able to take advantage of this new functionality in GeneSpring which will be very helpful to our joint customers," Julie Bryant, VP of business development for St. Joseph, Mich.-based GeneGo, said in a statement.

Here is something I came across recently, a relatively old article which I found on Bioinformatics Zen by Michale Barton. Simple, practical and worldly wise. Bioinformatics usually involves shuffling data into the right format for plotting or statistical tests. I prefer to use a database to store and format data as I think this make projects easier to maintain compared with using just scripts. I find a dynamic language like Ruby and libraries for database manipulation like ActiveRecord makes using a database relatively simple. Using a database however stops being simple when you have to deal with very large amounts of data. Here I’m outlining my experience of analysing gigabytes of data with millions of data points and how tried to improve my software’s performance when manipulating this data. I’ve ordered each approaches with I think is the most pragmatic first. The simple things Obvious but sometimes overlooked. 1. Use a bigger computer Using a faster computer might seem like a la...

CambridgeSoft's Business Partner in Kochi, India is hiring for multiple positions. If you know any appropriate candidates, with a chemistry or biochemistry background. The following is a list of available positions: Team Lead - coordinating the activities of small software development teams: http://www.cambridgesoft.com/careers/details/?Career=115 3D Team Leader : http://www.cambridgesoft.com/careers/details/?Career=228 Developer - Network Communications and Distributed Computing : http://www.cambridgesoft.com/careers/details/?Career=230 Developer Numerical Methods: http://www.cambridgesoft.com/careers/details/?Career=234 Senior Lead Developer : http://www.cambridgesoft.com/careers/details/?Career=225 Scientific Software Developer C++ : http://www.cambridgesoft.com/careers/details/?Career=14 Lead Developer E-Notebook : http://www.cambridgesoft.com/careers/details/?Career=81 E-Notebook Enterprise Support Analyst : http://www.cambridgesoft.com/careers/de...

The first effort to sequence a complete cancer genome has underscored the power of second-generation sequencing while further establishing the lack of a “killer software app” in the field. In the study, published this week in Nature , a team of 48 scientists at the Genome Center of Washington University and elsewhere sequenced a female patient’s acute myeloid leukemia genome and compared it to the genome of her biopsied skin as well as reference genomes to uncover 10 cancer-associated mutations — eight of which were previously unknown. The team used two high-throughput sequencing platforms — the Illumina Genome Analyzer and the Roche/454 FLX platform — and software tools such as Maq, Cross_Match, BLAT, and Decision Tree analysis. The team also did its own scripting and algorithm development in the course of the project, Rick Wilson, director of the Genome Sequencing Center at Washington University School of Medicine, said. The AML sequencing team applied several established soft...

The International Conference in Trends for Scientific Information Professionals Habitual attendees say that "it is the meeting to which they go to spot the trends, as well as the meeting that provides unparalleled opportunities for networking" Trends and networking will be high on the Nice agenda in October 2008. The ICIC meeting covers trends in the field of scientific and professional information with an impressive line-up of significant figures in the information world. Among the topics that will be covered and discussed by the 22+ speakers are: Tools for Competitive Intelligence ( e.g., mining tools, visualisation tools, analysis tools, etc ) Challenges for the information community over the next five years Changes in the information environment for patents, innovation and intellectual property Trends in Search Engines and Information Retrieval ( also see ) Case Studies in Data and Content Integration

The new hotness, fast, efficient, distributed version control system ideal for the collaborative development of software... Github , a source code management (SCM) repository based on git has exited beta and is ready for people to sign up. Git and github offer interesting opportunities for bioinformatics software development, and I think it’s worth taking a few minutes to explore them. There’s a free option too , so it doesn’t cost anything to sign up and play around. Github builds on git and takes the easy branching feature a step further to create a social software site. I know everyone and their dog is creating a social [insert verb]ing application/site, but you might find that that github’s approach can make a difference in your approach to software development. Github makes it possible to see who is creating branches of your project, visualised as a network, where branch and merge points are shown in a timeline. More on git and github Repository Formats Matter Moving from subver...

The Molecular Evolutionary Genetics Analysis ( MEGA ) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.

A leading provider of software for pharmaceutical discovery and development, today announced that the pharmacokinetics , dynamics, and metabolism science board at a top three pharmaceutical company named its software an "application of choice." As pharmaceutical companies face a significant number of patent expirations in the near future, there is a need to become more aggressive in research and development to fill the pipeline, sometimes with reduced R&D staff. Productivity tools in the field of pharmacokinectics , ADMET , chemical data visualization and analysis , etc. that leverage the expertise of the industry's scientific teams. It is believed that the difficulties facing some parts of the pharmaceutical industry will result in greater use of such tools as managers realize that the savings in time and money that can be achieved through their application vastly exceeds the cost of obtaining and learning to use them.

Yes i am talking about the development in the field of literature search and scientific publication search. Looking beyond NLP some of the advancements and service models based on NLP and other advanced methods. Today to the user's delight there are quite a few companies and organization that provide services that absolutely make an scientist life easy! These services revolve around customized alert services for selected search terms, specific research area of interest even more so pertaining to a list of custom key-word and search terms that the service providers allow the user to choose form. The scientist can simply subscribe to such service, sit back and wait for daily updates. The updates are provided on a day to day basis at his desktop. He gets abstract summarization , full text summarization so that he need not actually go through the ordeal of reading through pages of scientific literature. Some once else does the job for him and just pick up the right things that he woul...