This Week's Top Stories
As protesters occupy Wall Street, top academic groups in New York are getting ready to open one of the country's biggest genome centers in the city. With an expected price tag of $125 million, the New York Genome Center aims to be a major hub for genome sequencing and bioinformatics. The center hopes to attract biotech talent to a city best known as a force in the financial world--one of the reasons that it's drawn the ire of demonstrators who are fed up with the financial system.
The nonprofit center has been in the works for a while, with players behind the center talking to the media and seeking funding for the colossal endeavor. This week the center said that Illumina ($ILMN) and Roche--two major providers of genome sequencing technology--are contributing tech and expertise to the project. Early next year, the center is expected to get up and running in a gleaming new 120,000-square-foot building. The operation is expected to house not only the sequencing machines and other lab tools to study genomes, but also the data-mining and computational resources to help researchers manage and analyze the data, according to a release.
"We're looking to recruit Ph.D.s, mathematicians and computational biologists, to interpret the sequencing data and to assist researchers on a consulting basis," Nancy Kelly, executive director of the genome center, told Bio-IT World in an interview.
Bioinformatics, of course, has been a critical component to the genomics revolution, and many of the world's top providers of sequencing tools and services have been beefing up their computing capabilities as the volume of genome data skyrockets. Also, the center plans to use IT to facilitate its collaborations with academic groups and researchers at other institutions. It plans to play a role in training for genomics and bioinformatics professionals in New York as well.
New York's leaders in government and academic officials have been working on multiple new programs to boost the city's profile in the genomics field, building on an already strong cluster of pharmaceutical companies and research universities and hospitals. For instance, universities and research groups--including the New York Genome Center--are vying for $100 million to establish a science and technology campus in the city, Bloomberg has reported this week. The hope is that elevating the city's position in biotech will stimulate job growth in the life sciences.
Adding more computational biologists to the city's labor pool could be a nice hedge against lost jobs on Wall Street, which seems as unpopular as ever.
- here's the center's release
- read the interview in Bio-IT World
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Read more about: Illumina, DNA sequencing, bioinformatics
Thirteen hospitals in New York could see major investments in electronic patient records pay off in spades. Pfizer ($PFE) and four other large drug companies aim to pay the hospitals $50,000 to $200,000 every time the hospitals mine their databases and come back with a list of qualified patients for the drugmakers' clinical trials, Bloomberg BusinessWeek reported.
As pharma groups search for ways to make trials recruitment more efficient, the Partnership to Advance Electronic Patient Research (PACeR) has a pilot project in New York to improve the usability of electronic patient data for clinical researchers. Oracle ($ORCL) and Quintiles Transnational ($QTRN) are two firms helping to build the system required for the project, and large drug companies such as Pfizer, Roche, Merck ($MRK), Johnson & Johnson ($JNJ) and Bayer are backing the endeavor. The patient-recruitment effort, which could generate $75 million per year, gets started this month, according to the Bloomberg article.
While $200,000 might sound like a lot of dough for this type of service, consider that drugmakers stand to get hit with even higher expenses for study delays because of holdups in getting enough patients in clinical trials. Drug developers are already paying hefty sums to fund campaigns that use advertising and various forms of outreach to recruit patients. And trial recruitment falls onto a long list of logistical issues that developers face when trying to get a trial up and running in the U.S. and Canada, where clinical researchers have bemoaned the loss of revenue-generating trials to overseas sites such as India and Eastern Europe. This has created growing market for software firms and groups such as PACeR.
"This is going to be a game changer, making medicine more of a science and less of an art," John Murphy, senior director of clinical analytics for Quintiles, told Bloomberg.
The article points out that all kinds of ethical and privacy issues come into play when querying patient records for drug companies. For starters, the drugmakers aren't doing the actual queries, the hospitals are, and all the data that developers are given are stripped clean information that reveals the identity of the patient. Yet there's still plenty of fodder here--big drug companies paying hospitals for patient data, for one--to rile privacy advocates.
- check out the article
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Read more about: patient recruitment, electronic medical record, Pfizer, PACeR
R&D software maker Accelrys ($ACCL) has taken a bit of hit today after reporting financial results. The San Diego-based firm has sought growth through acquisitions over the past year and a half, and more buyouts are expected to scale up its business in the future, GenomeWeb reported.
During the July, August and September quarter, the company's non-GAAP revenue fell 9% or $3.7 million to $38 million, according to the firm's release. Non-GAAP net income was $5.4 million in the third quarter of 2011 compared with $5.7 million in the same quarter last year--another drop. Yet the third-quarter GAAP revenue--which includes the impact of the July 2010 buyout of Symyx Technologies ($SMMX) and the purchase of Contur in May--jumped 25% or $7.1 million from $29.1 million last year to $36.3 million.
Accelrys's stock fell by 4.85% to a close of $6.47 on Friday after the third-quarter results were released on Thursday.
While Accelrys has enlarged itself since last year, especially due to its merger with Symyx, PerkinElmer ($PKI) has been gobbling up R&D software companies over the past year such as Geospiza, CambridgeSoft and Labtronics. This gives PerkinElmer a potent answer to Accelrys's electronic lab notebook offering, as both CambridgeSoft and Labtronics offer competing products in the ELN market. Accelrys has tried to set itself apart from competitors this year with the releases of updated software, including its enhanced Discovery Studio and Cheminformatics products.
"I am pleased with the progress we made over the past quarter advancing our strategy, product roadmap and partner relationships. These efforts put us in a strong position to help our customers effectively manage the industry trends towards biotherapeutics development and the externalization of core research projects," Max Carnecchia, CEO of Accelrys, said in a statement. "We delivered two new releases that are fundamental to our enterprise R&D platform, further reinforcing our commitment to keep pace with scientific advancements."
- here's the release
- see GenomeWeb's coverage
- and the note from StreetInsider
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As drugmakers try to keep up with many key findings in scientific journals, personalized healthcare group Selventa and software firm Linguamatics have joined forces to streamline how important data from the literature are culled for further study, the companies announced last week.
Cambridge, MA-based Selventa (formerly Genstruct), which analyzes patient data for drug developers, brings to the alliance its expertise in a computable format for large-scale scientific data called biological expression language. For its part, Linguamatics, headquartered in Cambridge, U.K., is providing technology for I2E natural language processing, which will be used to corral important information from unstructured text much faster than any human could likely gather the information manually. Financial details of the companies' alliance weren't revealed.
Drug developers are faced with a growing body of scientific literature that offers potentially important information for their research. Scientists can spend hours poring over scientific texts or doing manual database searches to get to the findings they need for studies. Swiss drug giant Roche, for example, has provided its scientists with a tool called PubMed@Roche to map concepts rather than keywords in order to make its scientists' searches of PubMed efficient.
"Collaborating with Linguamatics will enable rapid yet comprehensive investigation of new areas of biology by extracting computable knowledge from unstructured text. This will lead to innovation on many fronts, such as next generation sequencing, where well-structured information for reasoning has been limited," David de Graaf, president and CEO of Selventa, said in a statement. "As a result, this will have the potential to provide a deeper, content-rich, scientific investigation to our partners, and ultimately help their future discovery efforts. We see a great potential for positive impact on future drug development decisions in areas such as translational medicine and clinical proof-of-concept stages."
- here's the release
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Read more about: bioinformatics, data mining, Roche, Selventa
It's a truism that the pace of progress is easier to predict in information technology than in biology. Why? Living organisms are complex and not easily manipulated, for starters. But now an international group of computer scientists and experts from other fields are embarking on a project to create a computer operating system of sorts for cells, potentially opening the door to more efficient creation of novel organisms that can do things that natural creatures can't.
In the field of synthetic biology, for example, there's an iterative process to develop a man-made organism. Researchers often have to start from scratch each time they build an organism, and that can require huge amounts of time and money. Think about having to create a new version of Windows every time you wanted to load software onto your computer. To hear the group at the University of Nottingham, that hypothetical scenario doesn't seem far off from the challenges of synthetic biology.
"We are looking at creating a cell's equivalent to a computer operating system in such a way that a given group of cells could be seamlessly re-programmed to perform any function without needing to modifying its hardware," Professor Natalio Krasnogor of the University of Nottingham's School of Computer Science said in a statement. "We are talking about a highly ambitious goal leading to a fundamental breakthrough that will, ultimately, allow us to rapidly prototype, implement and deploy living entities that are completely new and do not appear in nature, adapting them so they perform new useful functions."
The effort, which is being called "Towards a Biological Cell Operating System" (AUdACiOus), has also attracted experts from MIT, Arizona State University, Michigan State University, University of California, Santa Barbara, UC San Francisco, as well as researchers in Israel and Spain. The group believes that the project's tech, which will include models to predict the behavior of cells, could find use in medicine and cleaning the environment. No big surprises there given the diversity of the synthetic biology arena today.
- here's the University of Nottingham's story
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