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Optimer Pharmaceuticals Receives Milestone Payment From Cempra for Next-Generation Macrolide Antibiotic

Last Updated on Saturday, 24 July 2010 04:26 Written by admin Thursday, 8 July 2010 11:02

SAN DIEGO, July 8 /PRNewswire-FirstCall/ – Optimer Pharmaceuticals, Inc. today announced it has received a $500,000 milestone payment from Cempra Pharmaceuticals, Inc. pursuant to the terms of a licensing agreement between the companies.  The milestone payment was made as a result of Cempra’s continuing development of a next-generation macrolide (CEM-101) for the treatment of respiratory infections. Cempra licensed CEM-101 from Optimer and has successfully completed a Phase 1 study.

“The successful completion of the CEM-101 Phase 1 study further validates our OPopSâ„¢ drug discovery platform. We are pleased to see this compound progress into the next phase of development by Cempra,” said Pedro Lichtinger, Optimer’s President and CEO.

CEM-101 is a next-generation oral macrolide entering Phase 2 clinical development for the treatment of community-acquired bacterial pneumonia (CABP). Cempra has exclusive worldwide rights, except in Association of Southeast Asian Nations, or ASEAN, countries, from Optimer to discover, develop and commercialize macrolides from a library of more than 500 compounds, including CEM-101, originated from Optimer’s OPopS drug discovery platform.

In vitro and in vivo studies of CEM-101 have shown potent activity against S. pneumoniae as well as an extended spectrum of activity against community-associated methicillin-resistant Staphylococcus aureaus (CA-MRSA), M. avium and in animal models of malaria. These studies have also indicated that CEM-101 is active against atypical bacteria, such as Legionella, Mycoplasma and Ureaplasma and against gonococci and other organisms that cause genitourinary tract infections.

About OPopSâ„¢

Optimer’s OPopS drug discovery platform allows the development of potential drug candidates through carbohydrate mediated medicinal chemistry and enables the rapid synthesis of a wide variety of proprietary molecules. It includes GlycoOptimization, which enables the modification of a carbohydrate group on an existing drug to improve its properties, and De Novo Glycosylation, which introduces new carbohydrate groups on existing drugs to create new patentable compounds with improvement of pharmacokinetics.

About Optimer Pharmaceuticals

Optimer Pharmaceuticals, Inc. is a biopharmaceutical company focused on discovering, developing and commercializing innovative anti-infectives to treat serious infections and address unmet medical needs. Optimer has two late-stage anti-infective product candidates under development. Fidaxomicin is a narrow spectrum antibiotic being developed for the treatment of Clostridium difficile infection (CDI).  In two Phase 3 trials completed by Optimer to study the safety and efficacy of fidaxomicin for the treatment of CDI, fidaxomicin was statistically superior to vancomycin in global cure rate (defined as cure with no recurrence within four weeks of completing therapy) as well as statistically superior in reducing recurrences of CDI by up to 50% when compared with vancomycin, the only FDA approved product for CDI. Pruvel™ is a prodrug in the fluoroquinolone class of antibiotics being developed as a treatment for infectious diarrhea.  Optimer has also successfully completed two Phase 3 trials with Pruvel.  Additional information can be found at http://www.optimerpharma.com.

CLC bio’s enterprise platform wins award at Bio-IT World Expo in Boston

Last Updated on Sunday, 10 May 2009 08:32 Written by admin Sunday, 10 May 2009 08:32

Boston, Massachusetts, USA — April 30, 2009 — CLC bio’s enterprise platform for Next Generation Sequencing data analysis, CLC Genomics Server, has just been awarded the “Best of Show” prize at the Bio-IT World Conference & Expo 2009 – an award judged by a team of Bio-IT World magazine editors and leading industry experts.

Bio-IT World Editor-in-Chief Kevin Davies, PhD., comments, “Each year we go through a process where our judging panel debates the technical merits and likely business impact of the different technologies presented at the Best of Show awards. CLC bio’s success this year clearly reflects the importance of the incredibly exciting Next Generation Sequencing space, with a solution that is obviously gaining traction with it’s capabilities to handle the immense data management and analytical challenges required in this area.”

“Judging on several criteria, such as the importance of the problem being addressed and the elegance of the solution provided, it was clear to the judging panel that CLC Genomics Server, and the flexible plug-in structure it provides, delivers an ideal platform for researchers working with Next Generation Sequencing data.” says M. Michael Barmada, PhD. – member of the “Best of Show” judging panel and Director of the Center for Computational Genetics at the Graduate School of Public Health, University of Pittsburgh. “It’s nice to see complex computational algorithms and routines presented with an elegant interface in a user-friendly way, which lowers the technical barriers for all researchers working with high-throughput sequence data analysis.”

CLC Genomics Server is CLC bio’s advanced and powerful bioinformatics solution which is built upon a powerful and modern three-tier server architecture, that yields flexible options of executing centralized services, easy integration with other applications and services, powerful database communication and data integration, and secure access control framework and central action logging. Customers already using this enterprise platform, includes J. Craig Venter Institute, Albert Einstein College of Medicine, Veridex, and University of California – Berkeley. Read more about this solution here:

http://www.clcbio.com/index.php?id=1376

Posted under BioInformatics, Genomics & Pharmacogenomics, Grants and Awards, North America, Press Releases, USA and Canada  |  No Comments

A new approach to functional screening of siRNA knockdown

Last Updated on Wednesday, 26 November 2008 01:55 Written by Editor Wednesday, 26 November 2008 01:37


KINGSTON, England, Nov. 25, 2008-Guava Technologies, Inc. presented at the recent Molecular Targets & Cancer Therapeutics Symposium* information on their recent advancements that describe an experimental methodology and the new Guava® Simplicity Analysis Software which exploit the advantages of plate based flow technology. These technological improvements result in an overall process that can significantly expedite the drug discovery process by providing a means for extraction of key findings from the highly complex data sets encountered with functional screening of siRNA knockdown assays.

Solid tumors comprise genetically heterogeneous cell populations whose growth and survival depends on the complex interplay of distinct, yet overlapping, signaling networks. A major challenge in developing a course of therapy is determining which signaling nodes to target for a specific malignancy. Profiles from siRNA gene silencing are integral to mapping disease-specific signaling cascade(s) and provide insight to key targets for therapeutic intervention. Successful siRNA screening relies not solely upon optimizing transfection, but also cell analysis systems capable of high content screening (HCS) at the single cell level, within overall populations (sample well), and across multiple data sets.

The presentation describes how the Guava EasyCyteâ„¢ Plus System, with integrated Guava Simplicity Software, provides a revolutionary platform for secondary target validation and compound screening. Guava Technologies’ flow cytometers overcome the limitations of inference-based measurements of transfection efficiency and protein knockdown through direct quantitiative analysis of populations at the single cell level. The Simplicity Analysis Software’s intuitive architecture and ease of use facilitates the process of asking biological questions on multi-dimensional data sets through visualisation of user-defined parameters in the form of heat-maps. Most importantly, comparative results are displayed at the experiment level rather than on an individual well/sample basis.

Specifically, using the EasyCyte Plus System in tandem with Simplicity Analysis Software, 23 agents were identified that had growth restrictive properties although significant variation across cell lines was observed. Further targeted gene knockdown via siRNA confirmed the presence of both activators and inhibitors of Camptothecin-induced apoptosis as well as gene targets for growth arrest. Screens for apoptosis and cell cycle, as well as phospho-signaling intermediates, defined compounds with mechanisms of action similar to and different from Camptothecin. Cell-based assays for phenotype and function revealed a number of cooperative and antagonistic interactions between signaling intermediates, their respective cascades, and cytoactive agents.

Overall, the acquired multiplex data set is shown to provide a more detailed view on the behaviour of each of the test compounds with respect to apoptotic induction, cell cycle progression, and the signaling cascades that regulate these cellular responses to drug treatment. In total, this experimental methodology, when used in conjunction with Guava Technologies’ cell analysis platforms and Simplicity Analysis Software, significantly expedites the drug discovery process by providing a means for extraction of key biological findings from complex result sets.

If you would like more information on this application it is available for download from http://guavatechnologies.com/cm/Resources/Scientific%20Pubs.html. More information about the company and its products is available at www.guavatechnologies.com.

Guava Technologies, Inc., a privately held biotechnology company, is the leading provider of on-demand, easy-to-use single cell analysis systems. Guava® Systems, including the Guava® Personal Cell Analysis (PCA), Guava Auto CD4/CD4%, Guava® PCA-96 and Guava EasyCyteâ„¢ Systems, are integrated, fully optimised, microcapillary cytometry systems with embedded absolute cell counting capability. Used worldwide by the life sciences, biotechnology, and pharmaceutical industries, as well as clinical testing institutions (outside the United States and Europe), products from Guava Technologies have broad applications in scientific research and throughout the drug discovery and lead optimisation process, as well as for cell counting and optimisation of commercial biopharmaceutical production. Guava Technologies offers a variety of assays and dedicated software modules for the Guava Systems, enhancing the system’s overall ease-of-use.

* Guava, Guava Technologies Logo, and all other trademarks are property of Guava Technologies, Inc. * Guava® Simplicity Analysis Software is for Research Use Only. Not for use in Diagnostic procedures. * This symposium took place at the EORTC-NCI-AACR meeting in Geneva, Switzerland (21-24 October 2008)

Posted under BioInformatics, Cell-based Assays, Discoveries, Innovations and Patents, Equipment & Supplies, Europe, Industry News, News by Region, News by Subject, Press Releases, RNA Reasearch  |  No Comments

Virtual Screening Gives Drug Design a Boost

Last Updated on Wednesday, 19 November 2008 05:07 Written by Editor Wednesday, 19 November 2008 05:07

San Diego, CA (OBBeC) – Researchers at the University of California, San Diego, developed a unique computational approach to identify key compounds that could lead to new drugs to combat African sleeping sickness — a disease spread by the biting tsetse fly and caused by the parasite Trypanosoma brucei.

Around 150,000 people per year get African sleeping sickness. Unless treated, the illness is invariably fatal and with limited treatment available. The commonly used medicines to treat the disease are either difficult to administer, expensive, or toxic. For example, the widely used drug melarsoprol is essentially arsenic dissolved in antifreeze. Only one new drug to treat African sleeping sickness has appeared in the past 50 years. “The biomedical significance of new drugs to treat trypanosomal diseases, which occur mainly in developing countries, would be huge,” says Peter Preusch, of the National Institute of General Medical Sciences (NIGMS).
The research team led by computational biologist J. Andrew McCammon, have identified five compounds that could provide the solution for this problem. The compounds block the activity of the trypanosomal REL1 enzyme, which the parasite needs in order to survive. According to the press report, REL1 has a unique role in the trypanosome’s mitochondria, the organelles that provide the parasite with energy. The enzyme joins mitochondrial messenger RNA fragments, making them whole and functional. These messages are the blueprints for making the proteins that power the mitochondria. Without REL1, some of these mitochondrial proteins are missing, which slows energy production and kills the parasite.
The results appeared online this week in the Proceedings of the National Academy of Sciences.
New Computational Approach
The approach developed by McCammon’s group uses a combination of several computational tools. It starts with a detailed model of the biological target –REL1 in this case — derived from X-ray crystallography. It then uses biophysical principles to find all the ways in which the protein can twist, turn, and wiggle.
“We know that proteins aren’t static,” said Dr. Rommie Amaro, the lead author of the study. “They’re dynamic moving machines. The unique thing about this approach is that it allows full protein flexibility.”
Though, predicting the countless shapes that a large, complex molecule like a protein can adopt requires enormous computer power. A REL1 analysis done on a regular desktop could take years while those on supercomputers take a few days. The computers used in this study, explains Amaro, are among the most powerful in the country.
Once they know the dynamics, the researchers carry out a virtual screen of hundreds of compounds, testing their ability to stick to a key part of REL1. Compounds that stick tightly have a good chance of inhibiting the enzyme’s activity and killing the parasite.
“It’s rather like a child’s puzzle where one must put the cow-shaped piece into the cow shaped hole in the barnyard scene,” explains Preusch, who oversees computational biology grants at NIGMS, which partially funded the work. But like real cows, he added, molecules are in constant motion. “McCammon has developed methods that take these motions into account, as well as the changes in a protein’s shape that can occur upon binding.”
The virtual screen predicted that about a dozen compounds would bind tightly to REL1′s hot spot. Knowing that a slightly different version of one of these might stick even more tightly, the researchers searched a large database of existing compounds for structurally similar molecules.
When they tested their best candidates experimentally, five inhibited REL1. These five molecules, which block the activity of a crucial trypanosomal enzyme, can now serve as the basis for future drug design and discovery efforts.
Future Outlook
McCammon’s computational method has already proven its utility for designing other important drugs. His group used it to develop a model for a new class of drugs to treat AIDS that led to raltegravir, which the Food and Drug Administration approved in 2007. McCammon’s team also used the method to identify promising drug candidates for treating H5N1 avian flu.
McCammon’s team is now focusing on designing even better inhibitors of trypanosomal REL1. The goal is to tweak the inhibitors’ structures, making them bind even more tightly to REL1 and less tightly to related human enzymes. Binding to human enzymes makes an inhibitor less attractive as a drug candidate because the interactions could cause undesired side effects.
This work, says McCammon, “tells a story that may be of wide interest.” The computational approach not only could lead to improved drugs for treating African sleeping sickness, but it could be used to develop compounds for use against other illnesses for which we need better medications.

Posted under BioInformatics, ChemInformatics, Compound Screening, Drug-Like Compounds, HIV Research, North America, Press Releases, Targeted Libraries  |  No Comments

Otava develops virtual screening system

Last Updated on Tuesday, 11 November 2008 03:01 Written by admin Tuesday, 11 November 2008 03:01

Mathematical modelling in biology is often a problem with interactions estimation between a biomolecular target and small molecule compounds.

Knowledge of this interaction allows the interruption of certain processes in cells, for example it can impede diseases such as cancer.

This is why so many efforts focus on designing better models and algorithms for high-throughput virtual screening techniques.

Otava began developing its own virtual screening system in 2004 to incorporate entropy change that occurs during ligand-receptor binding into virtual screening protocol.

This project was initially restricted to model entropy change in harmonic oscillation approximation.

This model is closely related to quality of potential energy calculations.

Otava’s scientists designed a universal polarisable force field to achieve reasonable entropy change accounting (on the basis of unique empirical charges definition scheme).

Spanning entropies with traditional enthalpy calculations for free energy of binding prediction was inaccurate.

Adding ligands desolvation free energy that was calculated with modified GBSA method (up to 0.95 regression coefficient with experimentally derived data) improved the accuracy.

Further testing of the improved virtual screening system showed its efficiency depended on the nearest environmental water molecules, which are usually ignored in high-throughput virtual screening.

Otava’s scientists proposed a new algorithm of molecular docking code to implement fast and accurate water position finding.

Posted under BioInformatics, ChemInformatics, Europe, Press Releases  |  No Comments

DEFINIENS AND BIOSCAN TEAM UP FOR COOPERATIVE MARKETING EFFORTS

Last Updated on Sunday, 2 November 2008 05:52 Written by admin Sunday, 2 November 2008 05:52

Morristown, New Jersey / Munich, Germany – December 2, 2008 – Definiens, the number one Enterprise Image Intelligence™ company, has signed a co-marketing agreement with Bioscan, Inc., a leading developer of advanced imaging instrumentation for radiolabeled compounds.  Under the terms of the agreement, Bioscan and Definiens will conduct cooperative marketing activities and host joint workshops and events.  Customers will benefit through integrated training and implementation programs and streamlined access to the market-leading solutions offered by both companies. 

Non-invasive in vivo animal imaging offers researchers a window into living biological systems.  It provides the means to track a range of biological processes, from metabolism to receptors and gene-expression, and enables the effects of candidate pharmaceutical treatments to be monitored more accurately.  Recent improvements in molecular imaging technologies have made in vivo preclinical imaging increasingly important to researchers, and especially to those involved in the drug development process.  However, intelligent image analysis is required to extract meaningful insight from the prodigious amounts of data generated by advanced preclinical in vivo imaging systems.

Bioscan develops advanced instrumentation for the detection, synthesis and imaging of radiolabeled compounds used in life science research, molecular imaging, pharmaceutical development and nuclear medicine.  The company’s dual modality NanoSPECT/CT and NanoPET/CT in vivo animal imaging systems provide unparalleled insight into molecular function at the nanoliter precision level.  With these nano-nuclear imagers, Bioscan allows researchers to overcome the challenge of balancing resolution and sensitivity that has hampered the advancement of non-invasive imaging in preclinical studies.  

“Definiens and Bioscan share a commitment to developing the most advanced imaging technologies on the market,” said Dr. York Hamisch, Vice President of Imaging Technologies at Bioscan.  “This cooperative agreement will provide our customers with special access to Definiens’ image analysis technology, enabling them to extract information from their imagery with a high level of automation.”


Definiens provides life science organizations with software applications for analyzing and interpreting images on every scale, from cell and tissue-based assays to in-vivo imaging systems.  The company’s proprietary Definiens Cognition Network Technology® is context-based, emulating human cognitive processes to extract intelligence from images of all modalities, sizes,  and resolutions.  Definiens image analysis software complements Bioscan’s imaging systems, enabling researchers to extract additional quantitative and anatomical information from 3D images of small animal models.

 

“Increased adoption of non-invasive imaging is indicative of the life science research community’s move toward a systems biology approach,” said Manfred Voglmaier, Vice President of Business Development, Life Sciences at Definiens.  “Partnering with Bioscan provides an opportunity for Definiens to introduce its imaging technology to an established community of molecular imaging researchers.”

Definiens and Bioscan will continue to explore further opportunities for cooperation, which may include the co-development of user interfaces to incorporate Definiens software into Bioscan hardware.  Existing Bioscan customers will also benefit from introductory offers on Definiens applications beginning in late 2008.

Posted under BioInformatics, Collaborations, Europe, North America, Press Releases  |  No Comments

Tepnel Expands Genetic Services Portfolio with Addition of Illumina iScan Rapid Reader

Last Updated on Friday, 24 October 2008 10:36 Written by admin Friday, 24 October 2008 10:36

MANCHESTER, United Kingdom & STAMFORD, Conn.–Tepnel Life Sciences PLC (AIM:
TED) today announced that it has expanded its molecular genetic services
offering through the addition of Illumina’s iScan System, a next-generation
scanner that provides researchers conducting genetic variation studies with
significantly greater throughput and application diversity. This
announcement marks the first anniversary of Tepnel’s new pharmaceutical
services facility and makes Tepnel the first commercial provider of iScan
services within the UK.

Combined with Tepnel’s established range of upstream and downstream genetic
capabilities, the Company now offers a full suite of complementary services
from DNA extraction through to Bioinformatics. Illumina’s iScan platform
supports both human and non-human applications and is capable of generating
up to 225 million genotypes per day.

Tepnel also has a variety of other platforms and techniques for SNP-based
investigations for both human and non-human research and clinical
applications. This breadth of service enables Tepnel to provide a complete
solution from DNA extraction through to SNP genotyping and DNA sequencing,
all undertaken in accordance with Good Laboratory Practice (GLP).

“Tepnel can offer customers a broad portfolio of innovative genetic analysis
assays some of which are supported on our new high-throughput iScan reader,”
said David Scott, General Manager of Tepnel’s Livingston facility. “This new
addition to our service opens up the possibility to our customers of whole
genome association, focused content analysis, copy number variation analysis
and, epigenetics on both human and non-human samples, all within a
regulatory compliant environment.”

“Accelerating and expanding our molecular genetic services at this rapid
pace reflects our commitment to the long-term strategy of building Tepnel’s
market presence in the fast-growing sectors of
pharmacogenomics/pharmacogenetics and genetic disease disposition testing,”
said Allan Brown, Managing Director, Tepnel Research Products & Services.

About Tepnel Life Sciences plc

Tepnel Life Sciences (AIM:TED) is a UK-based international life sciences
products and services Group with two divisions, Molecular Diagnostics and
Research Products & Services. The Company has laboratories, manufacturing
and operations in the USA, UK and France with over 200 employees. Tepnel
provides test kits, reagents and services to two highly synergistic markets,
these being Molecular Diagnostics and Biomedical Research. The Company’s
strategy has been to identify high growth niche opportunities within these
multi-billion pound markets. Tepnel focuses on these niche operations with
internally developed products, patents, expertise and know-how as well as
strategic acquisitions, to develop a leadership position within these
defined market segments. For more information please visit www.tepnel.com.

Posted under BioInformatics, Clinical Trials, DNA Reasearch, Europe, Genetics & Pharmacogenetics, New Products, Press Releases  |  No Comments

CLC bio Signs Strategic Collaborative Agreement with J. Craig Venter Institute

Last Updated on Thursday, 9 October 2008 09:26 Written by admin Thursday, 9 October 2008 09:26

Cambridge, Massachusetts, USA — October 9, 2008 — CLC bio, a world leading full-service bioinformatics solution provider announced today an agreement with the J. Craig Venter Institute, a not-for profit genomic-focused research institute. The accord consists of a multi-year site license for the entire CLC bio bioinformatics suite of products. The goal is to implement CLC bio’s enterprise solution as a scientific platform across all JCVI sites. This enterprise solution will provide different research projects at JCVI with a coherent integration layer and a standardized way of developing custom software and specialized algorithms.

According to Granger Sutton, Senior Director of Informatics, “JCVI will benefit from implementing this enterprise solution, as it is a full enterprise platform that integrates, supports, and enhances workflows across different technologies and geographical sites. CLC bio’s software platform impressed our evaluators with its advanced features and intuitive, user-friendly interface.”

“We’re proud to announce this strategic partnership with JCVI, a leader in genomic research,” says CLC bio’s North America CEO Jan Lomholdt. “This site license agreement represents another stamp of approval of CLC bio’s solutions by a globally recognized institution in the scientific community. This partnership will lead to magnificent accomplishments in the scientific arena,” Lomholdt adds.

The enterprise solution CLC bio will be implementing at JCVI contains both server structure and support for all major database formats. This ensures a smart and efficient solution for sharing centralized bioinformatics data in a client/server architecture, where the server contains one or more databases and the clients are CLC bio’s workbenches.

CLC bio’s solution is a technological gateway that efficiently accesses all data and analysis in a single platform. With CLC bio’s enterprise solution all proprietary algorithms and solutions developed at JCVI can be accessed from the same bioinformatics platform, ensuring a streamlined workflow with minimal overhead and no tedious time-wasting procedures. CLC bio’s Developer Kit will enable JCVI to build targeted plug-ins for their internal use, while allowing JCVI to interact based on the same platform with worldwide collaborators.

About CLC bio
CLC bio is a world leading bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Focusing on Next Generation Sequencing downstream data analysis
Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, Collaborations, Europe, Press Releases  |  No Comments

CLC bio Partners with Illumina to Provide Next Generation Sequencing Analysis Technology

Last Updated on Thursday, 2 October 2008 06:01 Written by admin Thursday, 2 October 2008 06:01

Aarhus, Denmark — October 2, 2008 — Following an overwhelming reception of CLC Genomics Workbench 1.0, CLC bio is happy to announce the release of its next major version of their flagship product: CLC Genomics Workbench 2.0. Additionally, CLC bio has taken another important step in leading next generation sequencing data analysis by  becoming an Illumina Connect partner. Illumina Connect is a bioinformatics software partnership program established by Illumina, Inc. to advance data integration and analysis.

“CLC Genomics Workbench 2.0 provides scientists using Illumina’s Genome Analyzer with advanced downstream analysis,” says Jordan Stockton, Marketing Manager for Computational Biology at Illumina.  “Not only is it fast, but the new version of CLC Genomics Workbench offers alignment and assembly functionality that previously required larger investments in computer hardware. With its intuitive graphical interface, this application provides a simple desktop solution to biologists who might otherwise require the assistance of a dedicated bioinformatics professional.”

As an Illumina Connect partner, CLC bio has access to information in the ongoing development of Next Generation Sequencing tools, ensuring that CLC bio’s solutions will be able to fully support Illumina’s tools, including new releases.

Director of Scientific Software Solutions at CLC bio, Dr. Roald Forsberg states, “This release is inspired by the great advances in human genetics that are being powered by Next Generation Sequencing technologies, like Illumina. Large scale projects like the Cancer Genome Project and the 1000 Genomes Project are creating a vast amount of data that will transform biomedical research. However, before the revolution in human genetics can be fully realized by the research community there is a dramatic need for bioinformatics solutions that will allow biomedical researchers to handle and analyze sequencing projects at the human genomics scale – something we aim to solve with this and upcoming releases.”

CLC Genomics Workbench 2.0 will include several prominent new features, among these:

A new and extremely fast algorithm for the assembly of short reads

Lowering of the memory requirements that makes it feasible to perform reference assembly against all human chromosomes on a standard computer

Easy masking of genomic regions such as repeat or coding regions to lower the genomic complexity and facilitate the fast mapping of CHiP-seq data or exon captured data

Easy combination of data across platforms and experimental protocols so that e.g. single read and paired ends data are easily combined into one analysis
CLC Genomics Workbench is the first and only comprehensive analysis package which can analyze and visualize data from all major NGS platforms, such as Illumina’s Genome Analyzer, SOLiD by Applied Biosystems, 454 GS flx by Roche, and HeliScope by Helicos. CLC Genomics Workbench is platform independent, running on Mac OS X, Windows, and Linux – including 64bit versions.

To read more about CLC Genomics Workbench go to: www.clcbio.com/genomics
About CLC bio
CLC bio is a world leading bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Focusing on Next Generation Sequencing downstream data analysis
Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, Collaborations, Europe, Genomics & Pharmacogenomics, Press Releases  |  No Comments

First of 100 Arab Human Genomes Sequenced by Saudi Biosciences, Beijing Genomics Institute Shenzhen, and CLC bio

Last Updated on Tuesday, 9 September 2008 03:06 Written by admin Tuesday, 9 September 2008 03:06

Riyadh, Kingdom of Saudi Arabia — September 9, 2008 — An international consortium consisting of Saudi Biosciences, Beijing Genomics Institute Shenzhen, and CLC bio have in a joint effort performed an initial sequencing and analysis of the first Arab human genome, as part of a large project to sequence 100 Arab human genomes to map the unique genetic variations of the Arab population.

His Royal Highness Prince Ahmad bin Sultan bin Abdulaziz, Head of the Board of Directors at Saudi Biosciences, said “This marks the first milestone in our goal to pioneer the personalized medicine era in the Arab world, and the next step is to lead a large project to sequence 100 Arab genomes at high resolution no later than the end of 2010. Our ambitions are to make this project go beyond similar international efforts, both in terms of quality and quantity!”

Dr. Saeed Hussain from Saudi Bio Sciences, states, “We are extremely proud to present the first Arab human genome! This project launches the Kingdom of Saudi Arabia in to the small circle of nations who are currently in the process of building sophisticated databases of human genetic variation. This database is fundamental in the process of analyzing and understanding the specific genetic makeup of Arabs, which in turn will provide key knowledge to improve medical care for this large group of people.”

How was the project realized?
After Saudi Biosciences launched this project early 2008, an international joint collaboration with  Beijing Genomics Institute and CLC bio was organized.  A high quality sequencing of this genome was generated using Illumina’s Genome Analyzer platform. Afterwards the data was assembled and analyzed using CLC bio’s CLC Genomics Workbench.

“The fact that Saudi Biosciences have selected CLC bio among all the potential software providers, emphasizes that we are the world’s leading provider of genomics software solutions. We could think of no better opportunity to refine our software solutions, than a project like this, which is truly at the forefront of genomics research. This is indeed a unique and visionary project that we are excited and proud to be a part of.” said the Director of Scientific Solutions at CLC bio, Dr. Roald Forsberg.

The results, including analysis and identification of the unique variants of the Arab genome compared to African, European and Asian genomes, have been accumulated. The data are currently confidential but will be released following publication.

What is the impact of this project?
One of the most important goals of modern medicine and genetic research is the goal of tailoring medical care to an individual’s needs, based on information from the individual’s genotype or gene expression profile, so-called personalized medicine. Personalized medicine can offer huge advances in medical care but can only succeed if the genetic variation of humans can be accurately mapped.

The advent of a new generation of experimental techniques, has now given biomedical researchers the opportunity to map the complete genetic variation of large numbers of humans via full genome sequencing. The data produced from such efforts will provide an unparalleled amount of information that can be used to distinguish the unique groups within the human race, and help tailor medical care that targets the specific needs of different populations and individuals. Personalized medicine is thus on the brink of a major breakthrough.

However, the projects scheduled so far have aimed at characterizing mainly three populations – Africans, Europeans and Asians. This means that an accurate characterization and discovery of genetic variation in the Arab people can not be immediately expected and that the Arab populations may receive less of the benefits that will follow the advancement of personalized medicine.

This is why the Kingdom of Saudi Arabia wanted to start building an Arab human genomics database now, in order to scientifically explore the unique genetic composition in the Arab world. The database is fundamental in the process of analyzing and recognizing the distinct genetic makeup of Arabs, which in turn can provide knowledge to help stratify disease status, select between different medications and tailor their dosage, provide a specific therapy for an individual’s disease, or initiate a preventative measure that is particularly suited to that patient at the time of administration.

His Royal Highness Prince Ahmad bin Sultan bin Abdulaziz, Head of the Board of Directors at Saudi Biosciences, said “The Arab world was never an active participant in the large international projects in the field of genomics, and we believe that this should change. Working with an international collaborator such as Beijing Genomics Institute, an advanced institute in genomics studies, and CLC bio, the leaders in bioinformatics solutions with their recently released CLC Genomics workbench, we plan to participate actively in international efforts towards understanding the genomics basis of human diseases.”


About Saudi Biosciences

Saudi Biosciences (SB) is a leading biotechnology company in the Middle East. SB main goal is to  implement personalized medicine concept through studying the variations in Arabic populations. To achieve this goal, SB is sequencing 100 Arab genomes, exploring copy-number variations (CNV) and performing genome-wide association studies (GWAS) in collaboration with major institutes in Middle East.

About the Beijing Genomics Institute Shenzhen

The Beijing Genomics Institute Shenzhen (BGI) was founded in 1999. Since June of 2007, BGI has been headquartered in Shenzhen. It achieved international prominence as a center for sequencing the human genome. BGI completed one percent of the human genome for the Human Genome Project and ten percent of HapMap. Today the BGI staff of 500, led by Director Yang Huanming and Director Wang Jian, are in the forefront of genome research. Among other achievements, BGI has sequenced and mapped the rice and silk worm genomes. Current research includes sequencing of the panda genome as well as participation in the International HapMap project and the 1000 Genomes project.

About CLC bio

CLC bio is a world leading bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

  • Focusing on Next Generation Sequencing downstream data analysis
  • Development of bioinformatics software and hardware based on the latest scientific findings
  • User-friendly, integrated and intuitive cross-platform software solutions
  • Continuous focus on customer needs and superior customer service
  • Frequent product updates including the latest IT technologies and bioinformatics algorithms
  • A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under Asia, BioInformatics, Collaborations, Genomics & Pharmacogenomics, Press Releases  |  No Comments

TARGET DETECTIVE CONNECTS BIOLOGICAL TARGETS TO MOLECULES

Last Updated on Thursday, 28 August 2008 08:42 Written by admin Thursday, 28 August 2008 08:42

Tocris Bioscience (Bristol, UK) announced today the official launch of Target Detective, www.targetdetective.com, a new search facility that connects biological targets to research molecules.

Target Detective represents a significant development for pre-clinical researchers working in the Life Sciences field because for the first time scientists can connect receptor, enzyme, protein and gene data to Tocris products, through comprehensive ‘Target files’.

A Target File consists of a concise summary of the biological target, together with links to external sources of genetic and pharmacological information. Tocris products with activity at each target are listed here allowing rapid identification of the most relevant research tools.

To use Target Detective, start with any of the following biological search terms: Receptor (e.g. CB2), Enzyme (e.g. MEK), Protein (e.g. p53), Gene Name (Human, mouse and rat genes are currently searchable)

The ability to rapidly identify research tools for biological targets in this way is already proving to be extremely popular and at Tocris we are delighted with the response.  We will continue to add Target files and products and in the longer term we hope to make this the most useful resource for Life Science researchers on the internet.

Posted under BioInformatics, Europe, New Products, Press Releases  |  No Comments

CLC bio release white paper on the world’s fastest Next Generation Sequencing assembly algorithm

Last Updated on Monday, 28 July 2008 07:03 Written by admin Monday, 28 July 2008 07:03

Aarhus Denmark — July 23, 2008 — CLC bio has just released a scientific white paper which confirms, that, in benchmarking tests, CLC bio’s new algorithm for assembly of Next Generation Sequencing data is the fastest one available. Not only is CLC bio’s algorithm considerably faster, but it also provides a better quality of the results, compared to other algorithms benchmarked in the white paper.

Assistant Professor at Rutgers University, Dr. Todd P. Michael, states, ‘The speed of CLC bio’s new algorithm for reference assembly of Next Generation Sequencing data raises the bar to a level currently unmatched by any competitor. When CLC bio continues this impressive rate of development, and eventually also handles SOLiD’s Color Space analysis in the same convincing manner, this could easily become a de facto tool for scientists working with Next Generation Sequencing analysis.’

Instead of using around 3 to 4 hours assembling 8.5 million reads against a whole human genome, CLC bio’s assembly algorithm accomplished the same calculation in little more than half an hour, which means at least 5 times faster than the closest competitor.

For the assembly of large data sets, the increase in speed is even bigger: When assembling 86 million reads against the whole human genome, CLC bio’s assembly algorithm is more than 14 times faster, meaning an assembly normally taking almost 40 hours can be done in less than two! At the same time, CLC bio’s algorithm provides a better quality of the results delivered with more than 85% accuracy, compared to around 83% for the other algorithms in the white paper.

Another highly interesting aspect of this improved assembly algorithm is the modest requirements of physical memory – at no point during the benchmark tests did CLC bio’s algorithm require more than 8GB RAM.

The benchmark tests were conducted by comparing both 8.5 million reads and 86 million reads against a whole human genome, kindly supplied by the Beijing Genomics Institute. The data set for the benchmark tests was sequenced on Illumina’s Solexa platform and each read had a length of 35 nucleotides.

Once the assembly algorithm will be released in August, it will be available both in a command-line version on CLC bio’s Bioinformatics Cell platform and through CLC Genomics Workbench, which offers an intuitive graphical interface for analyzing and visualizing Next Generation Sequencing data. CLC bio’s white paper is free to download for everyone at www.clccell.com/ngs

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

  • Development of bioinformatics software and hardware based on the latest scientific findings
  • User-friendly, integrated and intuitive cross-platform software solutions
  • Continuous focus on customer needs and superior customer service
  • Frequent product updates including the latest IT technologies and bioinformatics algorithms
  • A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, ChemInformatics, Discoveries, Innovations and Patents, Europe, Genomics & Pharmacogenomics, Press Releases  |  No Comments

CLC Genomics Workbench – CLC bio releases Next Generation Sequencing data analysis solution

Last Updated on Friday, 18 July 2008 07:00 Written by admin Friday, 18 July 2008 07:00

Aarhus, Denmark — June 12, 2008 — Today, CLC bio released their new Next Generation Sequencing (NGS) solution, CLC Genomics Workbench, which incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of a typical NGS workflow.

CLC Genomics Workbench is the first comprehensive analysis package which can analyze and visualize data from all the major NGS platforms, such as SOLiD by Applied Biosystems, 454 GS flx by Roche Applied Science, Solexa by Illumina, and HeliScope by Helicos.

Director of Scientific Solutions at CLC bio, Dr. Roald Forsberg, PhD, states, “We set out to overcome two major challenges when analyzing Next Generation Sequencing data. One was to eliminate the analysis bottleneck by being able to analyze NGS data faster than it is produced. We overcame that by implementing an accelerated assembly algorithm in CLC Genomics Workbench which preliminary benchmark tests confirm is a very fast assembly algorithm. Secondly, we wanted to deliver user-friendly software which makes powerful NGS analysis software available to all biomedical researchers.”

In benchmark tests, CLC bio has assembled half a million 454 reads against the full E.coli reference genome in around 2 minutes on a dual-core computer with 1 gigabyte RAM. This speed-up, based on integrated SIMD high-performance computing technology, increases even more when using a computer with more CPU-cores and RAM. CLC bio expects to release a benchmark white paper in the near future.

CLC Genomics Workbench 1.0 takes full advantage of “paired end” data, and supports a number of features and work-tasks, such as reference assembly of genomes, de novo assembly of genomes, SNP detection using advanced models, multiplexing, and high-throughput trimming.

Having completed the first version of CLC Genomics Workbench, CLC bio is already pursuing an ambitious development roadmap, which will enhance future softwares with features such as Digital Gene Expression, metagenomics, clustering and assembly of EST and cDNA sequences, large amounts of genomics and transcriptomics downstream analyses, and workflow support.

CLC Genomics Workbench has already been chosen as Next Generation Sequencing platform for all Danish universities. To read more about CLC Genomics Workbench go to: www.clcbio.com/genomics

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

  • Development of bioinformatics software and hardware based on the latest scientific findings
  • User-friendly, integrated and intuitive cross-platform software solutions
  • Continuous focus on customer needs and superior customer service
  • Frequent product updates including the latest IT technologies and bioinformatics algorithms
  • A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, ChemInformatics, Europe, Genomics & Pharmacogenomics, New Products, Press Releases  |  No Comments

Beijing Genomics Institute signs global site license with CLC bio for Next Generation Sequencing software platform

Last Updated on Friday, 18 July 2008 05:34 Written by admin Friday, 18 July 2008 05:34

Aarhus Denmark, July 3rd, 2008 – Beijing Genomics Institute (BGI) has signed a global site license agreement for CLC bio’s Next Generation Sequencing solution, CLC Genomics Workbench. The site license covers all researchers at all BGI sites, both inside and outside of China.

Head of Bioinformatics Division at BGI, Ruiqiang Li states, “We have chosen CLC Genomics Workbench as our platform for analyzing Next Generation Sequencing data after testing several commercial solutions, because it’s simply in a league of its own when it comes to flexibility and the way the Next Generation Sequencing tools can be used together with our own algorithms. In an organization of our size – with seventeen Illumina GA analyzers, as well as two AB/SOLiD and three Roche/454 Next Generation Sequencing machines, all of them running at full capacity – efficient workflows are of critical importance. We can support and expand our workflows by giving our scientists easy access via the Workbench to our own in-house developed algorithms. In no time, CLC Genomics Workbench has proved amazingly popular with our internal researchers, due to the fast, user-friendly and versatile platform it provides.”

Director of Partner Sales at CLC bio, Michael Heltzen states, “We are most thrilled to have agreed on a global site license with one of the best bioinformatics and sequencing facilities in the world, only four weeks after our solution for analyzing and visualizing Next Generation Sequencing data was released. Furthermore, we are honored that the famous bioinformatics researchers from BGI have chosen our Workbench as a working platform for both our and their own algorithms, side by side. CLC Genomics Workbench will help the scientists at BGI with their daily research, including prestigious projects like the Giant Panda Genome Project and the 1000 Genomes Project.”

CLC Genomics Workbench is the first comprehensive analysis package which can analyze and visualize data from all the major NGS platforms, such as Solexa by Illumina, SOLiD by Applied Biosystems, 454 by Roche Applied Science, and HeliScope by Helicos. CLC Genomics Workbench takes full advantage of “paired end” data and supports a number of features and work-tasks, such as reference assembly of genomes, de novo assembly of genomes, SNP detection using advanced models, multiplexing, and high-throughput trimming. Read more about it at: www.clcbio.com/genomics

CLC Genomics Workbench is available for Mac OS X, Windows and Linux.

About Beijing Genomics Institute

Beijing Genomics Institute is one of the leading global Genomics Institutes in the world, established in July 1999. Since then, BGI has grown rapidly and is partner in a number of international consortiums, including partnerships with the Wellcome Trust Sanger Institute, NIH and NHGRI on the 1,000 Genomes Project. BGI now has a number of research locations including major sites in Shenzhen and Beijing.

BGI aims to advance the understanding of biology and medicine through the use of large-scale sequencing and bioinformatics analysis. The institute also offers sequencing services to the international community. BGI promotes the use of genome-scale scientific approaches and strongly supports collaborative efforts in order to achieve this goal.

For further information, please contact:
Jia Ye, Spokesperson
Beijing Genomics Institute, Shenzhen
Tel: +86 755 25273910
Fax: +86 755 25273620
E-mail yejia@genomics.org.cn

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

  • Development of bioinformatics software and hardware based on the latest scientific findings
  • User-friendly, integrated and intuitive cross-platform software solutions
  • Continuous focus on customer needs and superior customer service
  • Frequent product updates including the latest IT technologies and bioinformatics algorithms
  • A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under Asia, BioInformatics, ChemInformatics, Collaborations, Genomics & Pharmacogenomics, North America, Press Releases  |  No Comments

CLC bio moves to new Headquarters in Denmark

Last Updated on Tuesday, 15 July 2008 07:18 Written by admin Tuesday, 15 July 2008 07:18

Aarhus Denmark — July 10, 2008 — On July 1st, CLC bio moved their Danish headquarters to a newly built office building in the Katrinebjerg area – a fast growing Danish ICT community which also features high-tech companies Google, VMware, and B&O, to name a few – as well as the University of Aarhus and the new interdisciplinary nanoscience center, which is currently under construction.

CEO at CLC bio, Thomas Knudsen, states, “This is yet another big step up for us, having outgrown our previous location at the Science Park. Now we reside in a modern office building, where we occupy the entire top floor with a beautiful view of Aarhus and the bay. This move signifies the growth of the company, going from a startup to being an established company – and we’re not stopping here. Our new office leverages plenty of opportunities to grow in the future and we think the future is looking bright for our company!”

CLC bio was established in January of 2005, and has since grown to close to fifty employees, with offices in Aarhus, Denmark; Boston, USA; Nottingham, UK; Rio de Janeiro, Brazil; New Delhi & Hyderabad, India. Currently, CLC bio is working on establishing another new office in Asia, which is slated to open later this year.

CLC bio’s bioinformatics solutions have proven highly popular in a relatively short time span, with close to one million software downloads and more than 75,000 users in three years, since the first software release.

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

  • Development of bioinformatics software and hardware based on the latest scientific findings
  • User-friendly, integrated and intuitive cross-platform software solutions
  • Continuous focus on customer needs and superior customer service
  • Frequent product updates including the latest IT technologies and bioinformatics algorithms
  • A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, ChemInformatics, Europe, Press Releases  |  No Comments

CRELUX and ProQinase establish joint crystal-grade kinase protein and structures platform

Last Updated on Wednesday, 7 May 2008 05:30 Written by admin Wednesday, 7 May 2008 05:30

Munich and Freiburg, Germany, May 7, 2008 / b3c newswire / – CRELUX and ProQinase announced today that they have entered into a joint agreement to supply customers with crystal-grade protein kinases and readily available kinase complex structures.

Under the agreement, CRELUX and ProQinase will establish and continuously expand an off-the-shelf crystal-grade protein kinase portfolio, optimized and quality-controlled for successful crystallization. In addition, the two companies will work closely together to provide new crystal-grade protein or crystal structures, tailored to meet customers’ needs.

Recombinant protein kinases, optimized for crystallization, will be produced and exclusively marketed by ProQinase, while CRELUX will continue to provide customers with crystallization and x-ray crystallography services. CRELUX will support ProQinase by performing crystallization quality control for each crystal grade protein batch. At the same time, ProQinase will grant CRELUX privileged direct access to kinase crystal-grade protein.

“This new joint crystal-grade kinase platform offers tremendous advantages: It enables us to continue to focus on our core expertise – complex structure solution – while leveraging the expertise of ProQinase to significantly strengthen our capacities in protein expression,” commented Dr. Michael Schäffer, CEO of CRELUX.

“The combination of CRELUX’s expertise in protein crystallography and ProQinase’s know-how in kinase cloning and expression makes the two companies the partners of choice for all customers interested in kinase crystallography,” noted Dr. Christoph Schächtele, CEO of ProQinase.

CRELUX has used its state-of-the-art structural biology platform to solve more than 250 crystal and co-crystal structures for pharma and biotech companies. This platform encompasses all steps – from target cloning and expression all the way to high-throughput protein crystallization and in-house x-ray crystallography.

ProQinase, as part of its integrated protein kinase technology platform, offers more than 150 recombinant human protein kinases – all produced in-house – and provides all types of in vitro testing services, with more than 220 protein kinases.

Notes to editors

CRELUX GmbH ( www.crelux.com) provides fast and affordable access to co-crystal structures for biotech and pharma companies worldwide. Three dimensional structures of target-compound complexes are unique sources of information during the rational drug discovery process. Straightforward availability of structural data at an early stage of the drug development process significantly enhances productivity and success rates during hit selection, lead generation, and lead optimization. CRELUX has streamlined the processes of structure generation and solved hundreds of co-crystal structures using an integrated technology platform. In addition to customer designed projects crystallization conditions of numerous relevant therapeutic targets are available within the Off-The-Shelf Program of CRELUX. Off-The-Shelf target structures are delivered at a fixed price and short turn around times, facilitating affordable access to structural information.

ProQinase GmbH ( www.proqinase.com) provides an Integrated Protein Kinase Technology (iProKiTe®) Platform for preclinical drug development of protein kinase inhibitors. More than 150 highly active recombinant kinases are offered for sale and more than 220 kinases are available for in vitro testing services (HTS and selectivity profiling etc.). Cellular and in vivo test systems including orthotopic tumor models allow further testing of lead compounds. A Clinical biomarker analysis service supports the evaluation of clinical trials.

Posted under BioInformatics, Collaborations, Europe, Press Releases, Targeted Libraries  |  No Comments

CLC bio to collaborate with Microsoft on integrating life science technology

Last Updated on Wednesday, 30 April 2008 05:02 Written by admin Wednesday, 30 April 2008 05:02

Boston, USA — April 29, 2008 — Today at the Bio-IT World Conference & Expo in Boston, USA, CLC bio announced collaboration with Microsoft Corp. on integrating CLC bio’s extensive bioinformatics solutions with Microsoft’s software platform, for the benefit of companies, corporations, and institutions in the biotech, pharmaceutical, and life science sectors. CLC bio has already added support for Microsoft SQL Server in its database solution, CLC Bioinformatics Database, as well as support for Microsoft’s high-performance computing solutions, Windows Compute Cluster Server 2003 and Windows HPC Server 2008.

Dr. Rudy Potenzone, worldwide pharmaceutical industry technology strategist at Microsoft Corp. and director of the Bio IT Alliance, states,
‘We are delighted to work together with CLC bio, a member of the Bio IT Alliance and one of the world’s leading bioinformatics solution providers. This collaboration will ultimately help life sciences firms transition to the Microsoft platform throughout their research and development departments. CLC bio’s tools, fully integrated with the Microsoft Office System, increase ease of use and expand the number of potential users, while reducing administrative overhead and creating a lean workflow. Furthermore, CLC bio’s internationally renowned experts are available for consulting and customized development.’

Jan Lomholdt, Vice President at CLC bio, continues,
‘With our support for Microsoft’s server solutions, the first step in the process has already been taken. The second step is to further advance our collaboration in areas such as Next Generation Sequencing and high-performance computing, which ultimately can help realize the potential of personalized medicine. As a former member of Microsoft’s World Wide Advisory Council, I have first hand experience of the strength and potential Microsoft brings to the table with a collaboration like this, which of course is interesting for a company like ours.’

Windows HPC Server 2008, the successor to Windows Compute Cluster Server 2003, includes a common set of High Performance Computing productivity tools that reaches across desktop and clusters, including a new Parallel Computing Initiative for multicore development. CLC bio’s high-performance computing solution for servers and clusters, CLC Bioinformatics Cell, supports Microsoft’s Message Passing Interface (MPI) in order to run bioinformatics algorithms such as HMMER, ClustalW, and Smith-Waterman on Windows HPC Server 2008 installations.

All CLC bio’s solutions are cross-platform, running on Windows 2000, Windows XP, Windows Vista, as well as Mac OS X and Linux

About CLC bio
CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, ChemInformatics, Collaborations, North America, Press Releases  |  No Comments

World Premiere of Next Generation Sequencing solution from CLC bio

Last Updated on Friday, 25 April 2008 05:02 Written by admin Friday, 25 April 2008 05:02

Boston, USA — April 25, 2008 — On Monday, April 28, CLC bio will officially unveil their new Next Generation Sequencing solution, CLC Genomics Workbench, the first comprehensive analysis package which can analyze and visualize data from all the major Next Generation Sequencing (NGS) platforms, such as SOLiD from Applied Biosystems, 454 GS flx from Roche Applied Science, Solexa from Illumina, and HeliScope from Helicos. The World Premiere is at the Bio-IT World Conference & Expo,April 28 – April 30, at the World Trade Center in Boston, USA.

Vice President of CLC bio, Jan Lomholdt, states, Having experienced massive pre-release interest from people within the Next Generation Sequencing segment, we’re confident that our cross-platform NGS solution which includes an intuitive graphical interface, numerous downstream analyses, and support for all the major NGS platforms, will become a hit. Especially when taking into consideration that we have assembled half a million 454 reads against the full E.coli reference genome, in around 2 minutes on a Dual-core laptop with 1 gigabyte RAM. In other words: This is FAST!”

“There is an explosion of interest in the next generation sequencing field right now, and I’m confident that CLC Genomics Workbench will become a valuable tool for the rapidly growing number of users in academia and industry who are using these new instruments for an amazing range of applications,” said Bio-IT World Editor-in-Chief Kevin Davies, PhD. “We’re also delighted that CLC bio has choosen this year’s Bio-IT World Expo in Boston to announce and introduce this product to the scientific and informatics communities.”

CLC Genomics Workbench includes accelerated assembly of Next Generation Sequencing data through use of High Performance Computing technology, making the assembly process very fast. The genomes to be assembled can be of any size, only limited by the number of gigabytes of RAM available on the computer running the assembly.

CLC Genomics Workbench takes full advantage of “paired end” data, and supports a number of features and work-tasks, such as reference assembly of genomes, De Novo assembly of genomes, SNP detection using advanced statistical models, Digital Gene Expression, metagenomics, clustering and assembly of EST and cDNA sequences, large amounts of genomics and transcriptomics downstream analyses, and workflow support. Some of the mentioned features will be implemented in future releases.

CLC Genomics Workbench has already been chosen as Next Generation Sequencing platform for all Danish universities. CLC bio will release CLC Genomics Workbench to the public in late May. To read more about CLC Genomics Workbench go to: www.clcbio.com/genomics

About CLC bio
CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, Genomics & Pharmacogenomics, North America, Press Releases  |  No Comments

CLC bio and University of Copenhagen Sign Site License Agreement

Last Updated on Tuesday, 11 March 2008 05:05 Written by admin Tuesday, 11 March 2008 05:05

Copenhagen & Aarhus Denmark, March 11, 2007 — CLC bio and Department of Biology, Faculty of Science at University of Copenhagen, have signed a site license agreement for CLC bio’s premier bioinformatics software solution, CLC Combined Workbench, in combination with CLC bio’s Educational Suite. The deal runs for five years and is for several hundred seats, giving every researcher, student and teacher access to the software at all times.

The Head of Department of Biology at University of Copenhagen, Professor Dr. Lene Lange states,
‘We chose CLC bio as our solution provider as CLC Combined Workbench provides cutting edge algorithms and analyses of a high scientific standard, which is fundamental for our research. Also the wide range of tools available in this single application will eliminate a lot of tedious tasks, importing, exporting, and converting data between various applications – and thus help us improve our workflow, freeing up valuable time for research. We’re also looking forward to using CLC Educational Suite as a solid backbone for our bioinformatics courses.’

University of Copenhagen’s Department of Biology is organized in different Research Centers which are involved in international top tier research collaborations. They are funded from sources like the European Union and the Bill & Melinda Gates Foundation, among others. The many projects range from retrieval of ancient DNA from fossils (Center for Ancient Genetics), bioinformatics, gene regulations and SNP (Cancer Research), complex dependent mutations, primates genome evolution (The Genomics Group), whole genome sequencing of hyperthermophilic archaea bacteria (Archaea Biology Group), muscle biology (Copenhagen Muscle Research Center) to studies of how climate changes affects distribution of life on Earth (Center for Macroecology).

CLC Combined Workbench is a comprehensive software solution for advanced DNA, RNA, and protein analyses, containing all features of CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench in one, integrated software package. The program will replace the whole range of outdated and expensive tools, which the research centers have been using previously. CLC Combined Workbench is available for Mac OS X, Windows, and Linux

About CLC bio
CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under BioInformatics, Europe, Genomics & Pharmacogenomics, North America, Press Releases  |  No Comments

CLC bio provides bioinformatics educational solutions to Andhra University and 25 affiliated colleges

Last Updated on Thursday, 20 December 2007 02:42 Written by admin Thursday, 20 December 2007 02:42

Visakhpatnam, Andhra Pradesh, India – December 20, 2007 — CLC bio today announced the signing of a Memorandum of Understanding at an official ceremony at Andhra University, one of the most prestigious universities in India.

Under the agreement, Andhra University and 25 affiliated post graduate colleges will implement CLC bio’s educational solutions as an integrated part of their curriculum. CLC bio provides their top-line sequence analysis software, CLC Combined Workbench, to the university and colleges as well as training of the teachers and provision of customized education materials like PowerPoint slides, exercises, and more.

At the signing ceremony, Professor L. Venu Gopal Reddy, Vice Chancellor of Andhra University stated,
‘Its our great pleasure to announce this collaboration with CLC bio India. We are very happy to state that from now on Andhra University will be a dedicated user of CLC bio’s bioinformatics solutions in all our life science departments like Biotechnology, Microbiology, Biochemistry, Botany and Human Genetics. We consider CLC bio to be the premier bioinformatics solution provider in the world and this agreement will support education in Andhra University significantly. We are very proud to say that this agreement generates a significant competitive advantage compared to most other universities in India and abroad, in the field of bioinformatics and life sciences.’

Thomas Knudsen, Chief Executive Officer in the CLC bio Group continued,
‘I am honored to be attending the signing ceremony of this important agreement. I am sure that the use of our Educational Solutions – already implemented at a large number of universities in Europe, USA, and India – will bring Andhra University and the affiliated colleges a great step forward in their work to be among the top universities in India and abroad. I am also very happy with the extensive future collaboration which is a part of the agreement, ensuring that CLC bio’s Educational Solutions will always stay at pace with the fast moving educational sector in India.’

The software implementation and training will be carried out by CLC bio India which is headquartered in Hyderabad, Andhra Pradesh.

For more information on CLC bio’s educational solutions, go to:
www.clceducation.com


About CLC bio
CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms. CLC bio is an Apple solution provider and value added reseller.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

Development of bioinformatics software and hardware based on the latest scientific findings
User-friendly, integrated and intuitive cross-platform software solutions
Continuous focus on customer needs and superior customer service
Frequent product updates including the latest IT technologies and bioinformatics algorithms
A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Posted under Asia, BioInformatics, Press Releases  |  No Comments

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