Biomolecular computer promising in diagnostics

There's more progress in developing devices that use of biological molecules to compute information in our bodies to diagnose disease and release drugs. Researchers at the Weizmann Institute of Science in Israel have published findings in Nano Letters with their tiny computer that is designed to detect multiple molecular signs of disease.

"We envision nanometer-sized computing devices (made of biomolecules such as DNA) to roam our bodies in search of diseases in their early stage," Binyamin Gil, of the Weizmann Institute, tells PhysOrg.Com in an article published last week. "These devices would have the ability to sense disease indicators, diagnose the disease and treat it by administering or activating a therapeutic biomolecule. They could be delivered to the bloodstream or operate inside cells of a specific organ or tissue and be given as a preventive care."

The convergence of computer science and molecular biology, among other fields, has been hot as of late. Last month, a group from Caltech trumpeted their own progress in developing an advanced DNA computer with potential applications in disease diagnostics and research. Yet routine use of the devices in humans is likely years away and will require the tiny devices to hold together in the body long enough to do their job.

Published June 14 in Nano Letters, the Weizmann Institute group's research describes a biomolecular computer that can detect such molecular indicators as mRNA, small molecules and a DNA binding protein.

Related Article:

DNA computer tackles problems with code of life

BioTox buys CRO Bio-Quant

Two San Diego-based CROs are combining operations, and the buyer sees an opportunity to better serve its customers for preclinical services through integrating research software.

BioTox Sciences has agreed to purchase fellow CRO Bio-Quant from drug developer Apricus Biosciences ($APRI), which says today that it will reap at least $5 million up front from the deal and milestone payments of up to $20 million over the next 10 years. While BioTox President Sami Abundi says that the deal expands his firm's footprint in offering drug discovery and preclinical research services, he pointed out that there are synergies between Bio-Quant's and Bio-Tox's information technology systems.

"We can now take our clients' compounds through the preclinical drug development process and utilize state-of-the-art capabilities by integrating Bio-Quant's study execution software platform Intranet with BioTox's sponsor friendly and GLP compliant study data acquisition software, called iAdavantage, and thus accelerate the development process economically and effectively," Abundi said in a statement.

In fact, CROs around the world are boosting their investments in IT and developing their own proprietary software systems to help their customers in the life sciences industry streamline drug R&D. While many other companies are targeting the clinical-stage segment of the market, BioTox is taking this strategy to the preclinical phase, where there's also a lot of room to use IT to make multiple processes and experiments run more efficiently.

- check out the report from RTT News
- here's Apricus's release as it appears in MarketWatch

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Health informatics massive Optum changes CEOs

UnitedHealth Group's $27 billion health information and technology business, Optum, has a new chief. Larry Renfro takes the top job as former Optum chief G. Mike Mikan departs to head an undisclosed private equity firm. UnitedHealth announced the change last week.

Renfro, a former Fidelity Investments executive, who joined UnitedHealth in January 2009, steps into the top post at Optum amid a time of rapid growth in the business, which serves many types of healthcare stakeholders--including 400 life sciences companies--make use of analytics and health informatics to navigate challenges in their businesses. His group accounts for about a quarter of health insurance giant UnitedHealth's total revenue, Dow Jones Newswires reported, and consists of three business units, Optum Health, OptumInsight and OptumRx.

For life sciences companies, OptumInsight's technology and services become useful as the firms try to figure out which markets to pursue with their products, what reimbursements are likely to be, and what regulatory hurdles they will face. As health payers become choosier about the new drugs and other medical products they reimburse, life sciences companies have had to carefully weigh such factors into decisions about their R&D, for example.

"As the healthcare landscape continues to evolve, Optum's deep understanding of the diverse and changing needs of participants across the health system enables it to deliver collaborative solutions that provide the insights and care to help build sustainable health communities," Renfro said. "We have an outstanding team in place that has been effectively building the Optum platform to make it easier for clients to connect with the broad skills and expertise, innovative capabilities and end-to-end solutions across our businesses."

Still, Mikan's departure from Optum to get into the private equity game has been viewed as a negative for UnitedHealth ($UNH). "The main negative here is not that there was a surprise change in management, but rather the loss of one of the strongest managers at the company," Barclays Capital analyst Joshua Raskin wrote in a research note, as cited by Reuters.

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 Just one word... Bioinformatics

BGI Announces shade Genome Assembly provision

July 6, 2011 | SHENZHEN, CHINA-At the BGI Bioinformatics Software Release Conference today, researchers announced two new Cloud-based software-as-a-service offerings for next-gen data analysis. Hecate and Gaea (named for Greek gods) are “flexible computing” solutions for do novo assembly and genome resequencing. 

These are “cloud-based services for genetic researchers” so that researchers don’t need to “purchase your own cloud clusters,” said Evan Xiang, part of the flexible computing group at BGI Shenzhen. Hecate will do de novo assembly, and Gaea will run the SOAP2, BWA, Samtools, DIndel, and BGI’s realSFS algorithms. Xiang expects an updated version of Gaea to be released later this year with more algorithms available. 

Flexible computing, explained Xiang, is a more efficient cluster architecture than traditional Cloud. Jobs of different types are grouped on the cluster to make the most of computing power and address scalability issues. For instance, CPU intensive jobs are grouped; memory-intensive jobs are grouped; and input/output intensive jobs are grouped. 

Both the Hecate and Gaea services will run on the BGI compute cluster because “Amazon is slow,” Xiang said. Running the services on an in-house cluster also alleviates any internet access issues. 

Hecate is based on a series of distributed algorithms to recognize and simplify non-branching repeat-free regions of the genome, correct errors and resolve the ambiguous bubbles and short repeats, together with the distributed graph shrinkage algorithms to construct a linear DNA sequence. Based on BGI’s SOAPdenovo and SOAP2 algorithms, Hecate is more scalable than those algorithms alone. 

Xiang presented results from speed comparisons showing significant cost and time savings using Hecate for do novo assembly. Running SOAPdenovo on a single server for 70 hours resulted in 80% genome coverage at a hardware price of $150,000. Using 96 Hecate cores, the genome coverage increased to 84% in 42 hours at a price of $60,000. 

Gaea is designed to distribute resequencing computation to a cluster of nodes based on the Hadoop Streaming framework with personalized algorithm interfaces for SOAP and BWA. For the current version of Gaea (v 1.2), Xiang reported speed increases of 75x for SOAP2 and 90x for BWA using 100 cores. At 400 cores those numbers rose to 300x and 346x speed increases compared to running either algorithm on a single core. Xiang expects Gaea v 2.0 to see further improvements. 

Gaea is also optimized for a biomarker analysis toolkit that includes SOAPsnp, DIndel and realSFS for SNP calling, indel calling and gap alignment. 

More details about both products as well as a host of updated bioinformatics tools released at the event are available at soap.Genomics.Org.Cn. 

BGI Announces initial liberate of the Updated Bioinformatics Software

- Latest software enables more efficient and reliable results of a wide range of bioinformatics analyses.
- Download of Bioinformatics Software is free and early access is now available.
July 6th, 2011, Cambridge, MA and Shenzhen, China - BGI (previously known as the Beijing Genomics Institute), the largest genomics organization in the world, released its latest bioinformatics software, including its Short Oligonucleotide Analysis Package (SOAP series, etc.), Population Genetics Analysis Package, and Parallelization and Optimization of Traditional Tools. These provide the latest and most advanced solutions for biologists, and enable more efficient and reliable results of a wide range of bioinformatics analyses.
"These new capabilities enhance and complement BGI's existing state-of-the-art bioinformatics software applications for individual and population based research in animals, plants, microbes and human disease areas, meeting the requirements of leading research centers in the analysis and exploration of a wide range of biological data." stated Yingrui Li, Director of Science and Technology Department in BGI. "This is the first time BGI has provided detailed insights into our latest bioinformatics applications, pipelines and tools." He added.
The Short Oligonucleotide Analysis Package (SOAP series, etc.) has evolved from a single alignment tool to a suite of applications providing the complete solution to next generation sequencing data analysis. Currently, it consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder (SOAPindel), a structural variation scanner (SOAPsv), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool (SOAP3 -GPU). Today's release updated the SOAP series, including SOAP3 GPU/CPU, SOAPdenovo 2, SOAPindel (graph-based), and SOAPsv (assembly-based). The new software was released at a press conference where several international specialists in R&D bioinformatics platforms shared their views of the updated bioinformatics tools.
"SOAP3 is a GPU-based software for aligning short reads with a reference sequence. When compared with its previous version SOAP2, SOAP3 can be up to tens of times faster." stated Chuang Yu from the Science and Technology Department of BGI.
"SOAPdenovo2, the latest update of the extremely popular SOAPdenovo package, can assemble more accurately, continuous and completed genomes. Furthermore, there are other improvements which make SOAPdenovo2 more feasible for different situations and analysis." said Zhenyu Li, a specialist of the bioinformatics R&D platform at BGI.
When referring to the new SOAPindel (graph-based) tool, the Software Developer Jianliang Lu, said: "Indel Detection Based on Assembly perhaps offers the best chance for long indels and structural variations. Here we present SOAPIndel, based on de Bruiji graphs for calling longer indels more rapidly."
The analysis of genetic diversity within a species is vital for understanding evolutionary processes at the population and genomic level. Population genetics analysis tools, based on the large quantities of data produced from population genomics research, aid the detection and analysis of variation in populations more efficiently and accurately. "Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits." stated Haojing Shao, Technology Leader of Science and Technology Department of BGI."Most variants identified so far confer relatively small increments in risk. To take a comprehensive look at variants, we provide new software for analyzing indel or even SV in large sample size, low coverage next generation sequencing data."
Evan Xiang, R&D Director at the Flexible Computing Center of BGI, demonstrated how BGI's developed new cloud based distributed solutions, Hecate & Gaea, used to solve many of research problems in a "flexible" manner. He notes, "Hecate is a distributed solution and is very "flexible" on a cloud computing platform, which can reduce the cost of de novo assembly by more than 50%. In contrast, Gaea, a cloud based solution, is able to balance the workload over the entire cluster, which can improve the efficiency of cluster usage by more than 30%."
With the current rapid improvement of genetic and genomic technologies, the demand on storage and computing power has been increasing 10 fold every 12-18 months, which is far beyond the infamous Moore's Law. "To tackle these difficulties, BGI and its collaborators are working on GPU accelerated bioinformatics tools, including alignment and variation detection, for example. The improvements in speed are impressive -- the prototype version alignment tool is 10 fold faster than it's CPU counterpart, while SNP detection codes are about two magnitudes faster." stated Dr. Bingqiang Wang, Director of the High Performance Bioinformatics Center of BGI.
Finally, BGI announced they are providing free access to download and use the updated software. These latest packages complement and build upon many current tools and approaches for data analysis, which can meet the requirements of leading research institutions to explore a wide range of biological data. Moreover, the software can help to perform genome data analysis, including assembly, gene prediction, annotation, repetitive sequence analyses, SNPs and evolution analysis. Each year, BGI will host a series of workshops on cutting-edge bioinformatics to help researchers learn how to use the latest software advances and explore more deeply their biological data.
For information on early access to these updated bioinformatics solutions and applications, please visit: Http://soap.Genomics.Org.Cn/

About BGI
BGI (formerly known as Beijing Genomics Institute) was founded in Beijing in 1999 with the mission of supporting the development of science and technology, building strong research teams, and promoting the application of genomics in a variety of disease, agricultural, environmental and related fields. BGI has successfully completed a large number of projects. These include sequencing 1% of the human genome for the International Human Genome Project, contributing 10% to the International Human HapMap Project, carrying out research to combat SARS, being a key player in the Sino-British Chicken Genome Project, and completely sequencing the rice genome and the silkworm genome. In 2007, the headquarters relocated to Shenzhen. BGI-Shenzhen has completed the first Asian diploid genome, the cucumber genome project and the Panda genome project. Much of its research has been published in top international academic journals including Nature and Science. In conjunction with carrying out these projects, BGI-Shenzhen has established its own technical platforms based on large-scale genome sequencing, efficient bioinformatics analyses, and innovative genetic healthcare initiatives. These distinguished achievements have made a great contribution to the development of genomics in both China and the world. For more information, visit www.Bgiamericas.Com or www.Bgisequence.Com

Sequencing huge BGI advances in bioinformatics

BGI apparently isn't satisfied with being the largest genome sequencing outfit in the world. The Chinese sequencing giant has a host of new and updated bioinformatics software offerings, which appear to expand the breadth of depth of its capabilities in the sequencing market. The company provided a first glimpse at the technology in an event and release last week.
For starters, the Shenzhen, China-based company revealed its updated software used in assembling raw genomic data into coherent sequences. To make sequence information useful to scientists, the firm showed it latest tools for analyzing the data to identify abnormalities in the sequence that could aid in disease research. The company has also developed cloud-based applications to enable its customers to, say, assemble sequencing data more quickly and cheaply than traditional computing methods.
Already boasting a massive sequencing operation in China, BGI clearly sees the value in providing services and technology beyond decoding genomes for customers. As sequencing a genome--which can now be done for roughly $5,000--has become more of a commodity service, BGI and its competitors such as Complete Genomics ($GNOM) are jockeying to capture growing demand for technology and services that help customers such as drug R&D groups identify the gene mutations and other abnormalities in genomes that make sequencing information useful in their research.
"These new capabilities enhance and complement BGI's existing state-of-the-art bioinformatics software applications for individual and population based research in animals, plants, microbes and human disease areas," said Yingrui Li, director of the science and technology department at BGI. "This is the first time BGI has provided detailed insights into our latest bioinformatics applications, pipelines and tools."

IBM and ETH Zurich utilize Cloud Computing to Combat Increasingly Resistant Bacteria

ARMONK, N.Y., - 08 Jul 2011: IBM (NYSE: IBM) today announced researchers from science and technology university ETH Zurich and CloudBroker, a high-performance cloud computing company, have partnered with IBM to use cloud computing technology to conduct cutting-edge research focused on developing new antibiotics to fight disease.

According to the World Health Organization, the number of antimicrobial resistant pathogens is increasing dramatically, threatening treatments to tuberculosis, malaria and other now common illnesses caused by various bacteria. The study of bacterial proteins has become increasingly important as understanding the complex elements of bacteria can play a vital role in determining risks and determining drugs that can fight resistant strands.

Using IBM's SmartCloud Enterprise and an enhanced queuing and data management solution provided by CloudBroker, researchers from ETH Zurich's Institute of Molecular Systems Biology were able to identify nearly 250 potential virulence factors -- or molecules that are secreted by bacteria, viruses, fungi, or protozoa and then multiply within humans -- and create nearly 2.3 million three-dimensional models with nearly 30,000 background data packets to study the function of these harmful, disease causing pathogens.

Using the IBM Smart Cloud Enterprise, the team had access to almost 250,000 computing hours on a total of 1,000 parallel CPU's producing research on the structure of specific proteins found in the streptococcus bacteria which commonly causes strep throat in humans.

The open-source software Rosetta, which predicts and designs protein structures, protein folding mechanisms, and protein-protein interactions, was also deployed on the cloud. Through the use of these various technologies provided by IBM and CloudBroker, researchers were able to analyze the massive amount of data within two weeks, a task that would have taken several months without the use of IBM's cloud computing technologies.

"For our experiments, we need very high capacity in short time frames," said Dr. Lars Malmstrom, ETH Zurich's lead researcher. "Cloud computing allows to reserve this computing capacity whenever researchers need it, and it is available quickly. Research teams do not need to set it up or maintain it, and thus can concentrate better on their research."

About IBM Cloud Computing

IBM has helped thousands of clients adopt cloud models and manages millions of cloud based transactions every day. IBM assists clients in areas as diverse as banking, communications, healthcare and government to build their own clouds or securely tap into IBM cloud-based business and infrastructure services. IBM is unique in bringing together key cloud technologies, deep process knowledge, a broad portfolio of cloud solutions, and a network of global delivery centers. For more information about IBM cloud solutions, visit www.Ibm.Com/smartcloud.

About CloudBroker

CloudBroker GmbH is a start-up company located in Zurich, Switzerland, which provides easy access to high performance computing applications in the cloud. CloudBroker was founded as a spinoff company of the ETH Zurich in 2008. It offers a platform to easily deploy scientific and technical applications on cloud computing infrastructures that are then ready to be used immediately by researchers, with no additional time spent on installation or configuration of the software. CloudBroker also takes care of user management, testing and accounting of the software, allowing the users to just focus on their research and development. For details see also www.Cloudbroker.Com.

About ETH Zurich

ETH Zurich (Swiss Federal Institute of Technology, Zurich) has come to symbolise excellent education, groundbreaking basic research and applied results that are beneficial for society as a whole. ETH Zurich has more than 16,000 students from approximately 80 countries, 3,500 of whom are doctoral candidates. More than 400 professors teach and conduct research in the areas of engineering, architecture, mathematics, natural sciences, system-oriented sciences, and management and social sciences. ETH Zurich regularly appears at the top of international rankings as one of the best universities in the world. 21 Nobel Laureates have studied, taught or conducted research at ETH Zurich, underlining the excellent reputation of the institute. Www.Ethz.Ch/index_EN

IBM, others herd trial data to cloud 

Big-data attack targets schizophrenia 

Eli Lilly uses cloud computing for clinical data analysis 

IBM cloud aids scrap alongside superbugs

Big Blue's cloud has helped Swiss scientists in their hunt for clues about how certain bacteria form resistance against antibiotics and cause disease. It's perhaps the latest case where the tech giant ($IBM) has been aiding life sciences concerns in managing and analyzing biological or clinical data in the cloud.
For this latest feat, IBM--which has previously made the case that its cloud could help reduce clinical trial costs--worked with Swiss cloud computing start-up CloudBroker and researchers at the prestigious technical university ETH Zurich, according to IBM. With IBM's cloud and CloudBroker's queuing and data management software, the Swiss researchers analyzed a huge amount of data within two weeks. Without the technology, the analyses could have taken several months.
Indeed, IBM has made life sciences customers a key market for its cloud computing offerings for years. And as scientists compute massive amounts of data from disease proteins and genomes, clouds have proven to be useful in providing the needed computing capacity in short order. The technology also offers potential cost savings for managing and analyzing clinical data from drug trials. While developers are looking for ways to make their R&D run more efficiently, cloud computing has entered the discussion as one way to achieve this.
The scientists at ETH Zurich (from which CloudBroker spun off in 2008) used IBM's cloud to find about 250 virulence factors and conjure 2.3 million 3D models to gain a better understanding of disease-causing bacteria. For their study of streptococcus bacteria that cause strep throat, the scientists tapped nearly 250,000 computing hours on 1,000 parallel CPUs with Big Blue's Smart Cloud Enterprise.
"For our experiments, we need very high capacity in short time frames," Dr. Lars Malmstrom, ETH Zurich's lead researcher, said in IBM's release. "Cloud computing allows to reserve this computing capacity whenever researchers need it, and it is available quickly. Research teams do not need to set it up or maintain it, and thus can concentrate better on their research."