Bioinformatics Jobs

Introductory Statistics with R (Statistics and Computing)

Introductory Statistics with R (Statistics and Computing) R is an Open Source implementation of the S language. It works on multiple computing platforms and can be freely downloaded. R is now in widespread use for teaching at many levels as well as for practical data analysis and methodological development. This book provides an elementary-level introduction to R, targeting both non-statistician scientists in various fields and students of statistics. The main mode of presentation is via code examples with liberal commenting of the code and the output, from the computational as well as the statistical viewpoint. A supplementary R package can be downloaded and contains the data sets. The statistical methodology includes statistical standard distributions, one- and two-sample tests with continuous data, regression analysis, one- and two-way analysis of variance, regression analysis, analysis of tabular data, and sample size calculations. In addition, the last six chapters contain introductions to multiple linear regression analysis, linear models in general, logistic regression, survival analysis, Poisson regression, and nonlinear regression. In the second edition, the text and code have been updated to R version 2.6.2. The last two methodological chapters are new, as is a chapter on advanced data handling. The introductory chapter has been extended and reorganized as two chapters. Exercises have been revised and answers are now provided in an Appendix. Rating: (out of 25 reviews) List Price: $ 64.95 Price: $ 42.79 Share and Enjoy:  Read More →

BSAN – BioInformatics / ETL

TheLadders – Boston, MA – 104218- Are you one of this rare people out there with experience in biology, biochemistry or bioinformatics… /implement solutions Develop bioinformatics data models & informatics workflow solutions Develop annotated models – 0000 per year bioinformatics jobs in USA – Careerjet Share and Enjoy:  Read More →

GlaxoSmithKline sponsored PhD Studentship in Computational Biology, Department of Computing, Imperial College London

PhD Studentship: Applications are invited for an EPSRC/CASE funded PhD studentship supervised by Dr. Natasa Przulj at Imperial College*. *CASE studentships are awarded jointly to academic and industrial partners, and provide an exciting opportunity to work with cutting edge data and leading scientists from both research environments. The successful applicant will work both at Imperial [...] TheScienceJobs.com » Bioinformatics Share and Enjoy:  Read More →

AMSTAT – Scientist – Bioinformatics at Genentech (South San Francisco, CA)

in our South San Francisco, CA, headquarters: Scientist – Bioinformatics Responsibilities: Genentech seeks a highly … industry experience are essential. A good working knowledge of bioinformatics and biological concepts will be… View full post on Bioinformatics jobs | Simply Hired Share and Enjoy:  Read More →

Intern – Bioinformatics – Genentech, Inc. – South San Francisco, CA

Responsibilities: Candidate will work with scientists in both the Bioinformatics and Microbiology area and will have the opportunity to contribute to one of the… From ScienceCareers.org – 05 Jun 2010 07:21:16 GMT – job details – View all South San Francisco jobs View full post on bioinformatics Jobs | Indeed.com Share and Enjoy:  Read More →

Genoinformatics News

Mitrionics Announces Hybrid Computing Development System Based on SGI Altix XE 320 Quad-Core, Dual-Socket Server With Low Latency Front Side Bus (FSB) Interface

Mitrionics, Inc., developer of the Mitrion™ Virtual Processor and the Mitrion Software Acceleration Platform, today announced its Mitrionics MVP622 Hybrid Computing Server accelerated computing solution based on SGI® Altix® XE 320 server with a Quad-Core Intel® Xeon® 5420 Processor. The Dual-Socket Accelerated Server will include licenses for two Mitrion Virtual Processors (MVP), the XtremeData, Inc.™ XD2000i™ Front Side Bus (FSB) socket based accelerator hardware, each with dual Altera® Stratix™ III FPGAs, plus the Mitrion Software Development Kit with parallel programming language and working example code. This new MVP622 Hybrid Computing Server is the first of its kind that integrates hardware with an MVP, and a complete parallel programming environment in a single, off-the-shelf solution. “The world of computation is changing for good reasons,” stated Mike Calise, executive vice president and general manager of Mitrionics, Inc. “The industry has finally arrived at the point where hybrid computing is no longer relegated to exotic supercomputers. This package is commercially available and inexpensive, and since we’re solving the programming hurdle for FPGAs, makes the greenest accelerator alternative accessible to our customers.” “Mitrionics and SGI have worked together for years bringing the best Reconfigurable computing solutions to customers,” said Bill Mannel, director of server marketing, SGI. “By coupling the Altix ® XE 320 server with the new MVP Hybrid Computing Development System, we marry the advantages of the Altix XE 320, which seeks to optimize data center space while minimizing the power footprint, with the latest FPGA developments in the market today.” “We are starting to see increased adoption of accelerators of all types, and the FPGA offerings from Mitrionics might be particularly compelling for applications such as genome informatics or large-scale internet search,” said Addison Snell, VP of Tabor Research. “The fundamental difference for recent FPGA adoption lies in the reduced memory latency handled well by using a socket approach. These emerging, non-traditional application areas represent the highest potential growth in high-performance computing.” Mitrionics Hybrid Computing Development Systems are designed for industry, academics, government agencies, genome centers, data services providers, and independent software vendors (ISVs) that are interested in exploring the benefits of breakthrough hybrid computing architectures in practical workstation or server configurations. The applications that benefit from a system with at least two optimized compute processor types are those within genome informatics, Internet data processing, business process optimization, and most non 64-bit floating point HPC applications. These demanding integer-centric codes benefit from the variable bit width operations and fine grain parallelism inherent to Altera FPGA-based co-processors tightly coupled with Intel’s fastest CPUs. The system allows you to write accelerated algorithm code for a dedicated MVP data parallel co-processor within a fully integrated XD2000i “In-Socket Accelerator” (ISA) from XtremeData, Inc. This Altera based ISA is tightly “memory coupled” to the world’s fastest CPU’s from Intel through the industry standard front side bus (FSB) interface. The dual-socket servers can be configured to operate standalone or stacked in a cluster for highly dense green computing. The Mitrionics MVP622 Hybrid Computing Server is scheduled for availability in Q4 2008 with a list price of $24,900 USD. “The fast fabric and I/O capabilities of Stratix III FPGAs are validated in the Mitrionics platform by achieving FSB speed,” said Dr. Misha Burich, Altera’s senior vice president of research and development. “Stratix III FPGAs fully integrated into the XD2000i ISA demonstrate the benefits of the digital signal processing architecture for algorithms with floating point data.” Mitrionics MVP622 Hybrid Computing Server details – Dual Mitrion Virtual Processors – Mitrion Software Development Kit with one year email support – SGI Altix XE 320 dual socket server with single 2.5GHz quad-core Intel Xeon 5420 CPU, 4GB DDR2 800 (2X2 GB) memory – 250GB 7200RPM SATA Hard Disk Drive, with an optional second disk drive per system. – XtremeData XD2000i in-socket accelerator with dual Altera Stratix III 3S260E FPGAs, 16MB SRAM – CentOS 5.1 Linux Operating System – 1U Standard Rack Height – 650 Watt Autoswitching power supply – Optional interconnect and I/O expansion via on-board InfiniBand 4x DDR and a low-profile, half-length PCIe x8 Gen2 expansion slot – Optional second complete system in the same 1U chassis About Altera Altera Corporation (NASDAQ: ALTR) programmable solutions enable system and semiconductor companies to rapidly and cost-effectively innovate, differentiate and win in their markets. Find out more at www.altera.com. SGI – Innovation for Results™ SGI (NASDAQ: SGIC) is a leader in high-performance computing. SGI delivers a complete range of high-performance server, visualization and storage solutions along with industry-leading professional services and support that enable its customers to overcome the challenges of complex data-intensive workflows and accelerate breakthrough discoveries, innovation and information transformation. SGI solutions help customers solve their computing challenges whether it’s enhancing the quality of life through drug research, designing and manufacturing safer and more efficient cars and airplanes, studying global climate change, providing technologies for homeland security and defense, or helping enterprises manage large data. With offices worldwide, the company is headquartered in Sunnyvale, Calif., and can be found on the Web at sgi.com. About XtremeData XtremeData, Inc. creates hardware-accelerated database analytics appliances and is the inventor and leader in FPGA-based in-socket accelerators (ISAs). The company offers many different appliances and FPGA-based ISA solutions for markets such as decision support systems, financial analytics, video transcoding, life sciences, military and wireless. Founded in 2003, XtremeData is privately held and has two established locations. Headquarters are located in Schaumburg, Illinois, and a software development location in Bangalore, India. For more information, visit www.xtremedatainc.com. About Mitrionics Founded in 2001 and privately held, Mitrionics offers accelerated hybrid computing solutions. The Mitrion Virtual Processor (MVP) and the Mitrion Software Acceleration Platform accelerate a wide range of computing applications by exploiting the massively parallel and limitless internal bandwidth of standard FPGA architectures. Our products and services deliver a greener computing alternative, enabling 10x-100x performance increases and 90% less power consumption. Mitrionics’ customers are focused on adopting hybrid computing architectures to meet the exponential rise of compute requirements without adding additional watts to the computer system. The most noted users of MVP come from the areas of genome informatics, internet data processing and business process optimization. Mitrionics has key industry partnerships with processor companies Intel, AMD, Xilinx, and Altera, systems vendors HP and SGI, and accelerator module suppliers XtremeData and Nallatech. Mitrionics is privately held and located in Lund, Sweden and Los Gatos, CA. For information, visit the company Web site at www.mitrionics.com, or call 408-395-3247 408-395-3247, or email: info@mitrionics.com Mitrionics, Mitrion, Mitrion Platform, Mitrion Virtual Processor, and Mitrion Software Development Kit are trademarks of Mitrionics, Inc. All other trademarks are property of their respective owners. Share and Enjoy:  Read More →

Cited for two of the ‘best conferences’ in genome biology, CSHL gears up for 2nd annual Personal Genomes meeting

For decades, scientific meetings at Cold Spring Harbor Laboratory ( CSHL ) have been held in great esteem by scientists for their role in shaping the agenda of molecular biology. Their reputation for relevance continues, as evidenced by results of a survey of nearly 1,000 attendees of biology meetings over the last year. Published in the September issue of Genome Technology magazine, the survey identified two CSHL conferences in genomics as the best in their categories. Based upon a variety of criteria such as quality of speakers, presentation of new data and scientific results, networking opportunities, quality of posters, and overall “bang-for-the- buck” impact, CSHL’s “Biology of Genomes” meeting held annually in early May was a standout winner, ranked as the “most recommended” among general genomics meetings. A second CSHL meeting, “Genome Informatics,” held at the end of each October, was the “most recommended” in the Bioinformatics/Information Technology category. Excitement about 2nd ‘Personal Genomes’ meeting These results were announced as preparations reached their final stages for another genomics-related meeting at CSHL. From the 14th to the 17th of September, the Laboratory will host the second annual “Personal Genomes” meeting, which, according to its organizers, will build upon the excitement generated at the inaugural meeting last October. An editorial in the journal Nature appearing just after that gathering disbanded, late last October, confessed to initial skepticism about whether such a meeting was justified in view of the newness of the field and the paucity of results to date – at the time, the full genomes of only four people had been completed and made public. But, Nature assured readers after its reporter attended the meeting, participants came to understand that in fact the meeting was overdue, if for no other reason than the fact that “increasingly, private companies are offering personal genome scans and genetic tests for sale – and consumers are buying them.” As Nature opined, reflecting the view of many at the Personal Genomes meeting, “scientists can and should help the public sift through” newly available ( and often quite fragmentary ) genomic information generated for sale by a growing number of start-ups. At the second Personal Genomes gathering, which begins this evening and continues until Thursday, it is almost certain that participants will discuss these commercial developments, the pace of which has only accelerated in the interim. About the ‘Personal Genomes’ Meeting About 200 participants are expected to attend the four day-long “Personal Genomes” meeting, which has been organized by a renowned team of scientists, including Dr. George Church from Harvard University, and Dr. Elaine Mardis from Washington University, among others. The meeting will open with introductory remarks by CSHL’s Dr. James Watson, whose own genome was the first to become publicly available, making him the subject of last year’s inaugural meeting. Dr. Church, a genetics pioneer whose work integrates biosystems-modeling with synthetic biology and personal genomics, will give an overview of the field’s status in available technology and its current applications. Other notable technology-oriented speakers include Dr. Jonathan Rothberg from Ion Torrent Systems, Inc., and Dr. Steven Turner of Pacific Biosciences, who will discuss “third-generation” sequencing platforms that will soon enter the marketplace. Many genomics scientists working on cancer are trying to unlock the mystery of cancer’s molecular origins and make-up. Molecularly speaking, cancer is not a single disease. Two patients with lung cancer, for example, might have very different diseases stemming from different mutations, and so might not respond the same way to a drug. Dr. Mardis, who is the co-director of Washington University’s Genome Sequencing Center, will present on her group’s efforts to catalogue all mutations in a quartet of breast cancer patients. The keynote speech on Tuesday will be given by Dr. Thomas Caskey of University of Texas Health Science Center. “Dr. Caskey was one of the early planners of the Human Genome Project,” explains Dr. Mardis. “Now that we are at a stage when genomes are being sequenced in weeks and for medical purposes such as understanding disease causation, his talk will offer a very unique perspective on the past and the future of personal genomes.” The line-up of speakers includes other preeminent scientists in the field such as Dr. Richard Gibbs, Director of the Human Genome Sequencing Center at the Baylor College of Medicine who will describe his group’s work on sequencing genomes of patients with disease caused by defects in single genes; Dr. Steven Brenner, of UC, Berkeley, who is developing a public database of human genetic variation and its effect, drawing from databases, diagnostic laboratories, and the scientific literature to interpret human genomics data; and many others. A session on the ethical challenges presented by personal genomes will feature a panel of scientists, ethicists and science writers. “Fostering this type of cross-disciplinary discussion and debate is one of the strengths of CSHL’s meetings program,” says David Stewart, Executive Director of Meetings and Courses at CSHL. “This is where different fields are brought together and driven forward.” The results of Genome Technology’s survey would seem to bear him out. For more information on attending the conference or to find out about meetings topics and talks for potential news stories, please contact Peter Tarr ( tarr@cshl.edu ) or Hema Bashyam ( bashyam@cshl.edu ) at CSHL’s Public Affairs office ( 516-367-8455 516-367-8455 ). Cold Spring Harbor Laboratory ( CSHL ) is a private, not-for-profit research and education institution at the forefront of efforts in molecular biology and genetics to generate knowledge that will yield better diagnostics and treatments for cancer, neurological diseases and other major causes of human suffering. For more information, visit www.cshl.edu. Share and Enjoy:  Read More →

Chemoinformatics News

NOESIS TO BUILD UPON OPENEYE’S CHEMINFORMATICS TOOLKIT OECHEM

OpenEye Scientific Software, Inc., the developer of innovative molecular modeling and cheminformatics solutions for drug discovery research, and Noesis ChemoInformatics Ltd, a new developer of lead discovery software emphasizing knowledge extraction and management, today announced they entered into an agreement to allow the incorporation of OpenEye’s OEChem into Noesis’ NSISToolkit. OEChem, OpenEye’s programming library for chemistry and cheminformatics, will provide functionalities including SMILES parsing, SMARTS compiling, and substructure searching within NSISToolkit, the flagship product from Noesis that supports compound selection, molecular library and de novo design. “We are very pleased that OEChem’s speed, flexibility and robustness were among the key factors in Noesis’ decision to use our cheminformatics library within its NSISToolkit,” said Dr. Matthew Stahl, Senior Vice President of OpenEye Scientific Software, Inc. “Most of OpenEye’s technologies are made available as toolkits to enable the kind of custom solutions that Noesis creates.” He concluded, “OpenEye remains committed to providing scientifically rigorous toolkits to both end users and third party developers and we look forward to seeing the success of the new Noesis lead discovery tools.” Christos Nicolaou, Chief Scientific Officer and Founder of Noesis, continued: “NSISToolkit provides applications that aid in the identification and optimization of lead compounds through pharmaceutical knowledge extraction, reuse and management. Such high end applications make use of several fundamental cheminformatics functionalities including substructure mining, compound clustering and chemical scaffold extraction which, in turn, need quick, robust and accurate substructure searching capabilities and general molecular manipulation. The incorporation of OEChem allows NSISToolkit to expand its offerings and provide improved performance to match its users’ needs and expectations.” About OpenEye OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts and Strasbourg, France. It was founded in 1997 to develop large-scale modeling applications and toolkits. Primarily geared towards drug discovery and design, areas of application include chemical informatics, structure generation, docking, shape comparison, charge & electrostatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits – programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors, supports 64-bit processing, and runs on Linux, Windows and Mac OS X, as well as HP, IBM, SGI and SUN flavors of UNIX. For further information on the company and its products, see www.eyesopen.com. About Noesis CNI Noesis Chemoinformatics Ltd is a new research informatics company active in the chemoinformatics and general life sciences fields. The company has extensive experience in the R&D of algorithms and computational systems that support human experts in their decision making process. Noesis technology combines knowledge discovery and management techniques with expertise in biological and chemical data and processes to develop efficient chemoinformatics solutions. Its flagship product, NSISToolkit, addresses fundamental needs of the drug development industry, namely compound selection, lead identification and optimization as well as knowledge management and reuse. The company was founded in 2006 in Nicosia, Cyprus. For more information please see www.noesisinformatics.com. Share and Enjoy:  Read More →

GVK Biosciences (GVK BIO) along with Wyeth Research won the prestigious European Outsourcing Award 2009

GVK Biosciences (GVK BIO) along with Wyeth Research won the prestigious European Outsourcing Award 2009 for the Best New Partnership. The award was received by Manni Kantipudi, President, GVK BIO at a ceremony held at the Intercontinental Grand, Madrid, on 14th October. GVK BIO-Wyeth came out as winners amongst several competing entries. Earlier in the year, GVK BIO had filed its nominations under two categories “Best New Product” and the “Best New Partnership/Acquisition/Merger”. GVK BIO’s entry for the “Best New Product” was its innovative “Clinical Biomarker Database” developed together with a Big Pharma and the US FDA. “GVK BIO – Wyeth: Value co-creators” was GVK BIO’s nomination for the “Best New Partnership”. GVK BIO were declared finalists in both categories. “We are delighted to have won the Best New Partnership Award along with our partner, Wyeth Research. This award is recognition of the dedication and commitment of our employees in understanding and delivering to our customers’ expectations. We are proud that we have been considered alongside with Wyeth and thank them for their faith and commitment to this collaboration” said Manni Kantipudi, President, GVK Biosciences. The nomination for the Best New Partnership was put together by GVK BIO and Wyeth. It covered the GVK BIO-Wyeth trendsetting deal of 150 synthetic chemistry deal in 2006, further expansion of the collaboration to chemoinformatics and modeling. In 2008, Wyeth and GVK BIO entered into a collaboration based on a risk sharing model to identify and optimize lead series. About European Outsourcing Awards Launched in 2005, The European Outsourcing Awards recognize new and significant developments in Contract Services and reward successful companies for their outstanding contributions throughout the year. The Awards recognize excellence in R&D, marketing, business and technology across the pharmaceutical outsourcing, biopharmaceutical and clinical trial industries. The awards function is alongside the annual CPhI/ICSE/PMEC . About GVK BIO GVK Biosciences (GVK BIO) is Asia’s leading research services organization. GVK BIO provides a broad spectrum of services, stand-alone and integrated, across the R&D value chain. GVK BIO’s diverse portfolio of more than 100 customers includes Big Pharma companies, Agri & Life-sciences companies, leading biotechs and academic institutions. Spread across five locations in India, GVK BIO is headquartered at Hyderabad, India and employs 1500+ people to assist clients accelerate their research and success. Share and Enjoy:  Read More →