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Universiti Malaysia Sabah Biotechnology Research Institute partners with Synamatix to implement best-of-breed bioinformatics solutions 16th January 2008 KUALA LUMPUR, 16 January 2008 – Synamatix announced today a research collaboration and the licensing of cutting-edge bioinformatics technologies to Universiti Malaysia Sabah's Biotechnology Research Institute (BRI). The selection of bioinformatics solutions will be housed in a new centralised facility for BRI scientists to accelerate critical components of their biodiversity and marine biology research. The collaboration will also include a research partnership programme, which will enable opportunities for 'national interest' projects with Synamatix customers in the USA, Europe and Asia. Prof. Datin Dr. Ann Anton, Director of the Biotechnology Research Institute, said, "Synamatix was identified as our first choice partner based upon an extensive track record, validated technologies and international experience. Working with institutions such as Washington University Genome Sequencing Centre (USA), Beatson Institute for Cancer Research (UK) and also the Malaysia Genome Institute gave us confidence in their ability to contribute and add value to critical areas of research." Synamatix General Manager, Dr. Arif Anwar, stated, "We designed an integrated best-of-breed solution incorporating Synamatix technologies as well as third party software and hardware to meet the very diverse needs of BRI researchers. Applications will support and enhance extensive research activities in areas such as biodiversity and marine biology. By combining BRI's strengths in plant and marine research along with our domain expertise and cutting-edge technologies, we expect to achieve key research milestones within 12 to 24 months." BRI's newly completed Bioinformatics Resource Facility is the first in Malaysia to apply Synamatix's research, teaching and commercial partnership programmes with specific milestone targets identified over a three-year period. It is envisaged that this collaboration will help bridge the gap between innovative research in universities and practical applications in industry for Malaysia's growing biotechnology sector. About UMS Biotechnology Research Institute BRI, as a Centre of Excellence in the field of biotechnology, aims to promote research and development in biological or life sciences for the improvement of the quality of human life in medicine, food, agricultural science and environmental protection. BRI offers a wide range of postgraduate academic programmes by research and coursework in the field of biotechnology under a vibrant and well-resourced educational and research environment. About Synamatix The fundamental technology underlying Synamatix R&D is the proprietary "SynaBASE" platform. Applications built upon this database platform exhibit very significant improvement in analysis scalability, sensitivity and performance. Synamatix is a privately held bioinformatics company whose primary activities are ongoing R&D related to its core technology, and the support of its user base in the USA, Europe, Asia and Australia. Contact Patricia Chan Marketing and Communications Synamatix Sdn. Bhd. enquiries@synamatix.com www.synamatix.com |
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Synamatix Announces Collaboration with Emory University on Small RNA Based Brain Disease Studies 7th November 2007 Kuala Lumpur, 7 November 2007 – Synamatix announced today a research collaboration based upon neurological disease analysis with the Emory University School of Medicine in Atlanta, Georgia. Synamatix's role in this research will be to apply its novel SynaBASE™ and SXOligoSearch™ pattern-finding applications to process and analyse small RNAs generated from mouse brain cognitive disease studies. Dr. Peng Jin who is the project head from the Department of Human Genetics at Emory University stated, "We are interested in studying the small RNA profile in (the) adult mouse brain. Our aim is to conduct transcription profiling in mouse brains and identify novel RNAs for future studies in brain disease. Synamatix was approached as we believe that their technologies and early-stage experience in the analysis of data from 2nd generation sequencers would greatly assist us in enhancing our research agenda. So far, by utilising Synamatix's unique platform and approach, we have identified an increased number of novel hits, thereby adding immediate value to our project." Synamatix General Manager, Dr Arif Anwar, commented, "This project is bound to have a significant impact on the study of potential genetic factors in brain diseases. We are pleased to have the opportunity to work with Emory University, especially in supporting such a critically significant research area. Since the release of SXOligoSearch earlier in the year we have seen continuous improvement in its performance. We are currently developing new tools and applications to accomplish our goal of being a common informatics platform for any type of sequence data. This will further support and facilitate various projects that are leveraging recent advances in genomics technologies." SXOligoSearch, which is built upon the SynaBASE structured-network pattern platform, aligns complete reads rather than HSPs, resulting in higher specificity and sensitivity. This application is also able to handle low-quality reads containing numerous mismatches, insertions or deletions with high accuracy and superior performance. The SynaBASE engine is a novel approach towards enhancing the scalability, sensitivity and performance of genomics research without requiring the use of expensive specialist computer hardware typically required for such work. A trial version of SXOligoSearch is available online at www.synamatix.com. Various online bioinformatics tools based upon SynaBASE are also available for free at www.mgrc.com.my. About Synamatix The fundamental technology underlying Synamatix R&D is the proprietary "SynaBASE " platform. Applications built upon this database platform exhibit very significant improvement in analysis scalability, sensitivity and performance. Synamatix is a privately held bioinformatics company whose primary activities are ongoing R&D related to its core technology, and the support of its user base in the USA, Europe, Asia and Australia. About Emory University Emory University is located in Atlanta. Georgia, USA and is home to nine major academic divisions, numerous centres for advanced studies, and a host of prestigious affiliated institutions. The University encompasses a graduate school of arts and sciences; professional schools of medicine, theology, law, nursing, public health, and business; and two colleges. Contact Patricia Chan Marketing and Communications Synamatix Sdn. Bhd. enquiries@synamatix.com www.synamatix.com |
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454 LIFE SCIENCES AND MALAYSIAN GENOMICS RESOURCE CENTRE
ANNOUNCE A GENOMICS COLLABORATION TO ADVANCE
MICROBIAL AND MEDICAL RESEARCH IN ASIA 7th May 2007 BRANFORD, Conn., 7 May 2007 – 454 Life Sciences Corporation announced a collaboration today with Malaysian Genomics Resource Centre (MGRC) based upon applying high-speed DNA sequencing and bioinformatics technologies for the characterization of tropical organisms and diseases. 454 Life Sciences and MGRC will work together on applying the newly launched high-throughput Genome Sequencer FLX System™ (GS FLX) to spearhead the adoption and wide-spread deployment of cutting-edge genomics and bioinformatics projects in Malaysia. The collaboration was formally announced at a signing ceremony at the BIO International Convention in Boston, MA. The ceremony was officiated by the Honourable Deputy Prime Minister of Malaysia, Datuk Seri Mohd Najib Tun Abdul Razak. "Malaysia is investing significant resources in establishing itself as a regional hub for biotechnology research and industrialization," said Christopher McLeod, President and CEO of 454 Life Sciences. "We are delighted and excited to be involved as a partner with MGRC to help realize the full potential of genomics in Malaysia." 454 Life Sciences and MGRC will be collaborating on a number of high-profile projects from the Malaysian academic community. Specific examples that have already been earmarked include the sequencing of microbes with biotechnological and medical applications, as well as large scale-characterization of diseases that are prevalent in Malaysia and the region as a whole. Munirah Hamid, Executive Director of MGRC commented, "Genomics and bioinformatics have become fundamental, must-have technologies for advancing biological research. The 454 Life Sciences DNA sequencing platforms have enabled previously impractical projects to be pursued due to their combination of high accuracy, high throughput and lower cost of DNA sequencing." MGRC services are provided with the support of Malaysian Biotechnology Corporation (BiotechCorp), an agency under the purview of the Malaysian Ministry of Science, Technology and Innovation. BiotechCorp's objective is to support and accelerate growth of the Malaysian biotechnology industry. About 454 Life Sciences 454 Life Sciences develops and commercializes novel instrumentation for high-throughput DNA sequencing. Specific applications include whole-genome sequencing, RNA analysis and ultra-deep sequencing of target genes. The hallmarks of 454 Sequencing™ are its simple, unbiased sample preparation and massively parallel sequencing, which makes large-scale scientific projects feasible and more affordable. 454 Sequencing and the Genome Sequencer 20 System won The Wall Street Journal's top Innovation Award in 2005 and received an R&D 100 Editor's Choice Award as one of the most technologically significant products in 2006. The 454 Sequencing Center offers sequencing services directly to customers on a fee for service basis. Genome Sequencer systems are exclusively distributed for 454 Life Sciences by Roche Applied Science, a division of Roche Diagnostics. For additional information, please visit http://www.454.com. 454 Life Sciences Corporation is a majority-owned subsidiary of CuraGen Corporation. In March 2007, 454 Life Sciences, Roche Holdings, Inc. and an indirect wholly owned subsidiary of Roche Holdings entered into an Agreement and Plan of Merger whereby 454 Life Sciences will become an indirect wholly owned subsidiary of Roche Holdings if the merger is completed. The merger is expected to become effective in the second quarter of 2007 contingent upon regulatory approvals and certain closing conditions. For additional information regarding the merger, please refer to CuraGen's Current Report on Form 8-K filed with the Securities & Exchange Commission on April 2, 2007. |
Synamatix Announces Release of Bioinformatics Solutions for Second Generation Sequencers 24th April 2007 Kuala Lumpur, 24 April 2007 – Synamatix announced today the release of two new software applications designed to process and analyse data from large-scale re-sequencing projects conducted with second generation DNA sequencing platforms. Robert Hercus, Synamatix Managing Director, commented, "SXOligosearch™ and a modified version of SynaSearch™ have been released to address the growing explosion of data from the increasing use of the 454-Roche and Solexa-Illumina DNA sequencing platforms. These applications were developed as part of an ongoing strategy to complete a suite of high-throughput applications to process, analyse and integrate data from every type of second generation DNA sequencer." The first application, SXOligosearch, is designed to map short sequences such as reads from the Solexa-Illumina genome sequencer or oligonucleotide microarray probes. It offers a very high degree of flexibility in terms of handling a wide variety of read errors or mutations. In addition, more than a 100-fold improvement in performance compared to conventional tools is observed. Unlike other industry standard alignment tools, SXOligosearch aligns complete reads rather than HSPs resulting in higher specificity and sensitivity. It is also able to handle low-quality reads containing any number of mismatches, insertions or deletions with high accuracy and superior performance. A new version of SynaSearch, modified to process and map reads from the GS20 and FLX platforms from 454, has also been released. Careful optimisation has resulted in increased accuracy, specificity and a 200-fold improvement in performance compared to standard approaches. By using SynaBASE™ as a common platform, various types of reads can be mixed to increase coverage and deepen support for differences that are identified between data sets. Synamatix's other high-performance applications based upon SynaBASE, its unique structured network database platform, include SynaTree™, SXPRESearch™ and SXProbeDB™. About Synamatix The fundamental technology underlying Synamatix software applications is the proprietary "SynaBASE" platform. Applications built upon this database platform exhibit very significant improvement in scalability, sensitivity and performance. Synamatix is a privately held next-generation bioinformatics company whose primary activities are based upon ongoing R&D related to its core technology, development of new software applications, and the support of its user base in the USA, Europe, Asia and Australia. Contact Patricia Chan Marketing and Communications Synamatix Sdn. Bhd. enquiries@synamatix.com www.synamatix.com |
Universiti Industri Selangor Partners with Malaysian Genomics Resource Centre Sdn Bhd in a Bioinformatics Research and Collaboration Initiative 5th April 2007 Kuala Lumpur, 5 April 2007 – Malaysian Genomics Resource Centre Sdn Bhd (MGRC), today announced a partnership with Universiti Industri Selangor (Unisel) that will see the provision of the latest bioinformatics technology, consultation and support for the University's Bachelor of Bioinformatics programme. This programme is one of the first to be launched in Malaysia, based on this new industry-led format. According to Prof. Dr. Lokman bin Shamsuddin, Dean of the Faculty of Biotechnology and Life Sciences at Unisel, "We are excited to have the opportunity to work with an industry leader in bioinformatics and genomics research such as MGRC. This Malaysian company has shown significant growth both locally and internationally by securing leading universities, institutions and biotech companies worldwide as partners and customers." By utilising cutting-edge, high-speed bioinformatics applications from MGRC, Unisel will gain a clearer appreciation from an industry perspective on the overall direction and trends in bioinformatics around the world. For the duration of the collaboration, it is anticipated that Unisel and Malaysia will be able to leverage unique strengths in areas such as biodiversity and agricultural biotechnology research while students and researchers at Unisel will gain access to proven methods and approaches in contemporary bioinformatics research. The key objective for Unisel, in line with the national biotechnology directive, is to create and build a foundation and knowledge base to ensure continued growth of life sciences research in Malaysia. The only way to do this is through effective education and empowerment programmes with the support of proven successful industry partners such as MGRC. Such synergistic partnerships between academia and industry have proven to be a successful model in preparing students for positions within the biotechnology industry. Munirah Abdul Hamid, Executive Director of MGRC, said, "Unisel's pragmatic approach in course curriculum development and industry partnership programmes is essential to support the medium and long-term goals of establishing Malaysia as a leader in biotechnology research within this region." Multi-tier collaboration programmes such as that between Unisel and MGRC are seen as critical in assisting this overall direction and to convert academic research and innovation into tangible research of commercial value. About MGRC MGRC offers researchers worldwide online access to high-throughput bioinformatics applications, and genomic research services. The fundamental technology underlying MGRC's services is the proprietary SynaBASE platform. SynaBASE finds all patterns in genomic data and stores them into a network structure. Applications built upon this database platform exhibit very significant improvements in analysis scalability, sensitivity, specificity and performance. MGRC is a privately held bioinformatics company whose primary activities are based upon ongoing R&D related to its core technology and the support of its user base in the USA, Europe, Asia and Australia. About Unisel Unisel is a university fully owned by the Selangor State Government, specializing in technology based courses. Unisel networks with many industries especially those located in Selangor and this aspect is reflected in its curriculum. Since its inception in 1999 Unisel has become one of the most progressive universities in Malaysia. Faculties and academic centres in Unisel include the School of Biotechnology & Life Sciences, Faculty of Medical Science, the Lifelong Education Centre (UNISELEC) and many others. Unisel currently has two campuses which are at Bestari Jaya and Shah Alam. Contact Patricia Chan Marketing and Communications Malaysian Genomic Resource Centre patricia@mgrc.com.my www.mgrc.com.my |
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Synamatix Announces Release of SynaMer™ - A High-Speed Genome Read Processing Application
Kuala Lumpur, January 22, 2007 -
Synamatix announced today the release of SynaMer™, a bioinformatics application designed to complete ultra-fast and accurate processing of sequence reads for large scale genome assembly. The application was developed in collaboration with an unnamed genome research institute in the USA.
22 January 2007 The sequencing and assembly of new genomes is a core research objective for genome research centres. Having the capability to find longer over-lapping k-mers improves the quality of the final assembly as highly repetitive branch points can be spanned. In a recent project, SynaMer was used to process 23 billion bp of sequence data from the Macaque genome. The results were obtained in only 3.5 hours, producing as output, all over-lapping k-mers from the assembly reads, which, in this case, was the identification of all over-lapping 96-mers. Robert Hercus, Synamatix Managing Director, commented, "We are very pleased with the results and see this as the first of several major technical advances that we will be announcing for the enhancement and acceleration of genome assembly and genome re-sequencing." Synamatix's high-performance applications and SynaBASE™, its unique structured network database platform, can be licensed for onsite use or accessed online via "My Genomics Resource Centre" (MGRC - www.mgrc.com.my), a web-based bioinformatics service. About Synamatix The fundamental technology underlying Synamatix R & D is the proprietary "SynaBASE™" platform. Applications built upon this database platform exhibit very significant improvement in analysis scalability, sensitivity and performance. Synamatix is a privately held bioinformatics company whose primary activities are based upon ongoing R&D related to its core technology and the support of its user base in the USA, Europe, Asia and Australia. Contact Patricia Chan Marketing and Communications Synamatix Sdn. Bhd. enquiries@synamatix.com www.synamatix.com |
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Synamatix announces licensing of SynaBASE to Washington University Genome Sequencing Center 3rd April 2006 Kuala Lumpur, April 3, 2006 - Synamatix today announced that Washington University Genome Sequencing Center (WUGSC) has licensed SynaBASE™ and associated applications for use in high-throughput genomic analysis for internal research projects. The Center will also apply selected Synamatix applications towards enhancing quality control of data from newly sequenced genomes. |
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Synamatix Touts Analysis Speed with Intelligent Database 19th January 2006 January 19, 2006 - Life scientists are constantly dealing with the explosive growth of genomics and proteomics data and the need for ever-more sophisticated analysis of this data. |
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HP Powers 'My Genomics Resource Centre' Itanium® 2-based HP Integrity cluster server delivers the critical computing resources for Malaysia’s first online bioinformatics applications platform for the global life sciences research community 25th October 2005 Kuala Lumpur, October 25, 2005 - Hewlett-Packard today announced it has successfully implemented the Itanium® 2-based HP Integrity rx4640 cluster server for Malaysian Genomics Resource Centre (MGRC- www.mgrc.com.my), the country’s first and only online bioinformatics applications provider, which is branded as “My Genomics Resource Centre”. This multi-million dollar deal effectively underlines HP’s leadership position as an innovator and provider of highly scalable IT solutions for the life sciences industry. |
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My
Genomics Resource Centre (MGRC) licenses Synamatix Technologies to
Beatson Institute for Cancer Research (UK) 8th September 2005 Kuala Lumpur, September 8,
2005 - The Beatson Institute for Cancer Research (UK) has
licensed Synamatix technologies via “MGRC - My Genomics Resource
Centre” (www.mgrc.com.my), an
online bioinformatics services platform and partner of Synamatix. MGRC
services will be used to support the Beatson Institute’s research focus
on the cell and molecular biology of cancer. Prof. Keith Vass, Head of
Bioinformatics at the Institute, stated that, “the performance of
Synamatix technologies via MGRC meets our requirements for a fast and
sensitive genome analysis platform. We are particularly excited in
applying the unique capabilities of these tools in performing fast
searches across large phylogenetic distances.” |
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Synamatix Subsidiary, Malaysian Genomics Resource Centre (MGRC), Goes Live! 27th June 2005 Kuala Lumpur, Malaysia, June 27, 2005 - Synamatix, a Malaysia-based bioinformatics company, today announced that its subsidiary, Malaysian Genomics Resource Centre (MGRC), an online service provider platform for high-throughput sequence analysis tools, is now operational. The ASP platform will be branded as “MGRC - My Genomics Resource Centre” (www.mgrc.com.my) reflecting its primary aim of servicing the wide and varying needs of individual scientists and
researchers worldwide. |
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Salary
surveys, genetic
discrimination bills, and sequence analysis June 2005 (Genome Technology) One year ago in Genome Technology, our cover story was the magazine’s second annual salary survey, which offered results from the data provided by 1,180 readers. As we reported at the time, our readers’ data indicated that the life sciences field was moving away from the economic problems that had plagued it in the preceding couple of years; layoffs were down, raises were up, and salaries seemed to be moving in the right direction. This year, our cover story is once again our salary survey, and results suggest that the field continues to stabilize. Layoffs and pay cuts were comparable to their rates in the previous year, and salary ranges for the most part stayed fairly consistent. But we also find that a small portion of readers who received a raise last year don’t expect one this year. Responses to a new question about future plans indicate that scientists are often surveying the field for other opportunities: fully 40 percent of respondents who say their primary task is structural biology expect to leave their current job within a year. For that and loads more data, check out this year’s salary survey, starting on p. 24. In the news last year was a short article about Francis Collins’ push to get involved in personalized medicine. Collins made the argument that without significant legislative changes to protect people from genetic discrimination, major initiatives would not get off the ground. In the year since, the NHGRI director has continued to make his argument. At the ASHG meeting last October, Collins sat down with reporters to talk about the idea of a US-based large-scale cohort study similar to what the UK is attempting to do with its Biobank. Such a project could have a tremendous impact on medicine, Collins contended, but added that even suggesting such a thing would not be feasible without legislative support. This year the Senate has once again passed a genetic nondiscrimination bill — its second such attempt — but at press time there was no word on whether the bill would get through in the House of Representatives, where a similar bill stalled in 2003. In another news story last year, GT looked at Synamatix, an up-and-coming data analysis company based in Kuala Lumpur, Malaysia. In the year since, the company has continued to get attention, and recently launched a new module called FragBase, a pattern-recognition technology designed to prioritize and study relationships between sequences. The company says this particular application will help it establish a position for handling short sequence reads — a need that is expected to grow exponentially as genome sequencing becomes more affordable and technologies such as single-molecule sequencing take hold but produce shorter and shorter reads than their capillary cousins. Coming Up: Next Month in GT |
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Toolkit: Looking to ‘$1,000 Genome', Synamatix Launches FragBase Assembly Module
28th March 2005 (BioInform) The days of spending only $1,000 to sequence an entire human genome may be five years or more away, but Synamatix of Kuala Lumpur, Malaysia, is taking steps to establish itself as the data analysis company of choice for next-generation sequencing technologies. The company recently launched FragBase, a new module in a line of products built upon its “pattern-aware” data storage and management technology. The core of this technology platform, SynaBase, uses pattern-recognition technology to assign “significance” to certain sequence patterns and then stores the relationships between these patterns. Because the database stores each of these patterns only once, in a hierarchical structure, entire genomes can be stored in a much smaller amount of space than in relational databases or flat files, and can therefore be searched much more quickly, according to the company. Right now, the core application areas for the company’s technology have been in comparative genomics and high-throughput genomic searching, but Synamatix hopes to lay the groundwork for widespread adoption of its methods in future years. One area that Synamatix has identified as a good fit for its approach is next-generation sequencing methods currently under development at companies like 454, US Genomics, Solexa, and others. These methods promise to greatly speed the sequencing process, but one potential bottleneck is in the assembly of large amounts of sequence data. Truly personalized medicine won’t be practical if physicians require server farms to process their patients’ genome sequence data - regardless of the platform that generated it. FragBase was developed in collaboration with an undisclosed US company developing a next-generation sequencing platform, according to Arif Anwar, vice president of Synamatix. It’s been adapted to assemble “very large numbers of very small bits of DNA” - less than 100 base pairs. Current assembly algorithms rely on sequence alignment and are thrown off by repetitive regions. According to Synamatix, FragBase uses pattern recognition to overcome that problem by identifying repeat regions in advance. Contig coverage is assessed based on the company’s “significance” classification. “People are now moving toward the $100,000 genome in a year or two, and maybe the $1,000 genome will be attainable in four to five years. That would be a goo d timeline to hit, and we’re ready for that,” Anwar said. Apparently, Synamatix is not alone in planning ahead for the $1,000 genome. In mid-March, more than 50 people tuned in for a webcast that the company presented on the subject. Anwar added that the company is reaching out to other developers of high-throughput sequencing systems for potential partnerships. “We’re talking to everyone in this market,” he said. “We’ve made it a real key focus area, so there’s no one we’re not talking to. We’re not going to wait around.” - BT Copyright © 2005 GenomeWeb LLC. All Rights Reserved. |
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Malaysian Company Synamatix, speaks at the Internationally Acclaimed UK Bioinformatics Forum on Successful Strategies in Bioinformatics 8th March 2005 London, United Kingdom, 8th March 2005 - Synamatix, Malaysia’s pioneer global bioinformatics company was invited to speak at the internationally acclaimed UK Bioinformatics Forum. The focus of the Forum was to explore and examine successful strategies adopted by leading bioinformatics businesses around the world. A total of eleven companies were selected to present at the event, which included industry giants such as GE Healthcare Informatics, Accelrys, LION Biosciences and IBM Life Sciences. Synamatix, founded by Robert Hercus (the brainchild of ‘Touch ‘n’ Go’ - the world’s first pre-paid toll payment system), has achieved significant R&D and commercialisation milestones since commencement of operations in June 2002. Over the last year, the company’s technologies (centred on its core IP, SynaBASE™ - a structured network database for biological data), have demonstrated superior scalability and performance speeds beyond that achievable by conventional bioinformatics tools. According to Dr. Arif Anwar, Vice President of Synamatix, this was not the only reason behind the company’s numerous successes and milestones. Speaking at the Forum, Arif went on to say that “instrumental to Synamatix’s successes was not only the novel ultra-high-throughput capabilities of its technologies but also a number of macro-factors unique to Malaysia.” The strategic positioning of the company in Asia, the low development costs and an active Malaysian Venture Capital market were fundamental catalysts to a ‘fast-to-market’ development of Synamatix’s novel technologies. “The combination of this along with a supportive public sector backbone under the auspices of the Ministry of Science, Technology and Innovation (MOSTI) enabled Synamatix to convert tax break and grant incentives such as its Multimedia Development Corporation R&D Grant Scheme (MGS) grant of RM2.86 million (US$753,000) into real opportunities on local, regional and international fronts”, said Managing Director, Robert Hercus. Since commercialisation of SynaBASE and its ultra-fast analysis applications (SynaSUITE™) in March 2004, Synamatix has been focused on penetrating into the highly competitive markets of the USA, Europe and secondary markets such as Australia and the Asia Pacific region. In recent months, Synamatix has successfully demonstrated to industry experts the unique capabilities of its technologies in breaking through critical research bottlenecks associated with the management and analysis of large volumes of complex biological data. The company is proud to have an unspecified number of late-stage partnership and collaboration discussions with industry leaders in the pharmaceutical and biotechnology sectors, including various bioinformatics and genomics research institutions based in the USA, Europe and Australia. The validation and fast completion of its technologies, the low cost base coupled with sufficient funding in Asia have facilitated Synamatix in further expanding into new market opportunities via the creation of a subsidiary - Malaysian Genomics Resources Centre (MGRC). Its unique online offering of high-throughput, low cost bioinformatics services (currently branded as zoomagene.com) has allowed it to tap into unrealised market opportunities existing in academia and burgeoning small to medium sized entities (SMEs) prevalent in the Asia Pacific region. Synamatix’s endeavours over the past 12 months have provided the Malaysian company with international recognition as a world class contributor to the global bioinformatics industry. About Synamatix Sdn Bhd About Malaysian Genomics Resource Centre Sdn Bhd |
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M'sia shoots for standards in life sciences Thursday, October 28 2004 2:59 PM (CNETAsia) KUALA LUMPUR, Malaysia--Four Malaysian companies have joined hands to set up the country's first bioinformatics benchmarking center in a bid to harmonize local research with similar worldwide efforts. Based in Cyberjaya, Malaysia's designated high-tech industrial zone, the center is the result of a collaboration between the Multimedia Development Corporation, bioinformatics firms Synamatix and the Malaysian Genomics Resource Center, as well as computer giant Hewlett-Packard. "This represents an important milestone towards the development of bioinformatics technologies within the Multimedia Super Corridor and establishing Malaysia at the forefront of biotechnology development in Asia-Pacific," said Jamaludin Jarjis, the country's minister of science, technology and innovation. The main aim of establishing the new facility is to evaluate the performance of local bioinformatics technologies against global standards, said Arif Anwar, Synamatic's vice president. The science of bioinformatics gained prominence in the 1990s and involves the use of computers to analyze and make sense of complex life sciences data for things like drug research. However, according to Arif, a key issue in this industry is the lack of standardization between biotech firms across the world. "The current issues facing life sciences today is that there is a wide array of bioinformatics applications, often with many different approaches for a single research area," he said. "This current trend has resulted in very few consistent standards in bioinformatics, which has in turn made it difficult to validate and compare results." "More often than not, the first application becomes a default standard which subsequent applications are benchmarked against. But there is no mathematical verification that the default approach is in fact the best standard," Anwar said, adding that the center aims to work with the global life sciences community in deriving benchmarks for biotech applications. The center now provides a hosted online application for Malaysia companies to analyze genomic data. Arif claimed comparable technologies cost millions and are therefore out of reach for the majority of
scientists working in academia and smaller biotech firms. This service will initially be offered to
Malaysian companies only but it will subsequently be expanded to include other players in the global
life sciences market, he said. |
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Launch of Malaysian Genomics Resource Centre Sdn Bhd
and the Establishment of Malaysia's First Global Centre for Bioinformatics Benchmarking in the MSC 20 October 2004 KUALA LUMPUR, Malaysia, 20 October, 2004 - Malaysian bioinformatics company, Synamatix Sdn Bhd has announced today the establishment of Malaysian Genomics Resource Centre Sdn Bhd (MGRC) and its planned initiative in providing a bioinformatics ASP (Application Service Provider) service (zoomagene.com) for life scientists and researchers worldwide. As part of this, an announcement was also made on a strategic alliance between the Multimedia Development Corporation Sdn Bhd (MDC), Hewlett-Packard Sales (M) Sdn Bhd, Synamatix Sdn Bhd and MGRC in establishing Malaysia's first globally accessible Bioinformatics Benchmarking Centre. HP will supply the necessary hardware, including the latest HP Integrity servers running Itanium 2 processors powering Synamatix technologies (SynaSUITE). The Centre will be used to evaluate the performance of bioinformatics technologies against global industry standards. These key events represent important steps towards the development of bioinformatics technologies within the Multimedia Super Corridor and establishing Malaysia at the forefront of biotechnology development for the Asia Pacific region. The milestone announcements were made at an industry and press event officiated by the Minister of Science, Technology and Innovation (MOSTI) YB Dato' Dr. Jamaludin b Dato' Mohd Jarjis in Kuala Lumpur. Distinguished guests included YBhg Datuk Dr. Mohamed Arif Nun, CEO of MDC and YBhg Tengku Dato' Dr. Mohd. Azzman Shariffadeen, Chairman of Encipta Ltd (Investment arm of MIMOS). The event was also graced by industry leaders including Prof. Ernest Feytmans, Head of the Swiss Institute of Bioinformatics (one of the world's foremost bioinformatics institutions) as part of his official visit to HP (M) and Synamatix Sdn Bhd. In his opening speech YB Minister, Dato' Jamaludin Jarjis said "Malaysia has made significant advancements in the development of biotechnology industries [including bioinformatics and biodiversity exploitation] since 2001." The release of Synamatix's SynaSUITET and its global acceptance as a breakthrough technology for genetic data management and analysis as well as the establishment of MGRC and the Bioinformatics Benchmarking Centre is validation of the progress made in recent years. At the event, Dr. Arif Anwar, VP of Synamatix Sdn Bhd, spoke of the strong support the company has received under the auspices of the Malaysian Government (MOSTI) in the form of investment via Encipta Ltd. (investment arm of MIMOS) and as a grant recipient of RM2.86 million from MDC's MSC Grant Scheme (MGS). As emphasized by YBhg Datuk Dr. Arif Nun, "such mechanisms are put in place by the Malaysian Government to provide the necessary infrastructure to support and facilitate growth in high-tech industries. However in order to be effective and successful, it is in the end the private sector which must take the lead in R&D and global competitiveness." Since commencing its R&D operations in 2002, Synamatix has been successful in developing the world's first structured network database system for storage and ultra-high-throughput analysis of biological data. Synamatix claims to have outperformed some of the world's most powerful (and expensive) supercomputers and computing clusters. The company is now in partnership discussions with some of the leading pharmaceutical, biotechnology companies, universities and genomics research institutions in the US and European markets. As part of a new initiative by Synamatix, MGRC has been established with the primary objective of providing much needed ultra-high-throughput analysis tools (powered by SynaSUITE) to individual life scientists and researchers around the world. Comparable technologies tend to be priced in the vicinity of millions (USD) and therefore are out of reach for the majority of scientists working in academia, institutions and biotech SMEs (small to medium size enterprises). The primary focus is to empower scientists, via a cost effective ASP model (zoomagene.com), with the capabilities of accelerating discovery and de novo research. MGRC will also conduct and publish its own genomics research and will collaborate with industry research partners on certain projects. A key step in advancing MGRC (zoomagene.com), as it is for any new bioinformatics product and service, is performance benchmarking against industry standards. This need has resulted in the proposed establishment of a Bioinformatics Benchmarking Centre, which will utilise the MSC Innovation Centre and Hewlett-Packard industry know-how in the testing and benchmarking of Synamatix technologies. Bioinformatics Benchmarking will be part of the services offered by Solutions Assessment and Development Centre (SADC) at MSC Innovation Centre. SADC, a fully furnished test facility ready with network and communication infrastructure, proven test methodology and stringent quality measures for testing applications will subsequently offer benchmarking services to the wider global life sciences market. This collaboration, initiated with an official signing ceremony between YBhg Datuk Dr Arif Nun, CEO of MDC, Mr. TF Chong, Managing Director of HP (M), and Mr. Robert Hercus, Founder and Managing Director of Synamatix and MGRC, marks a significant step forward towards industry and government collaboration in biotechnology in Malaysia. About MDC The Multimedia Development Corporation Sdn Bhd is responsible for driving the development of Malaysia Knowledge industries under the auspices of the Multimedia Super Corridor (MSC). MSC is Malaysia's comprehensive ICT and Multimedia initiative bridging together the realms of ecology and technology set to revolutionise the nation's approach in developing its industries. Development of MSC has been planned over three phases commencing with its launch in 1996 and culminating in 2020 with Malaysia being firmly established as a model of leadership in the Information Age, in line with the government's Vision 2020. MSC is a test-bed area with outstanding infrastructure encompassing the Kuala Lumpur International Airport, the two "intelligent" cities of Cyberjaya and Putrajaya, the technology test-beds of Technology Park Malaysia, UPM-MTDC, KL Tower and the Petronas Twin Towers (KLCC). MSC is also an integrated logistics hub with its most recent infrastructure initiative being the establishment of BioValley, a biotech cluster situated in Cyberjaya. The MSC Innovation Centre, located at the heart of the MSC, serves to encourage continuous innovation of flagship applications. It is the central knowledge hub and common meeting place for participants of the innovation cycle, i.e. researchers, developers, inventors, vendors and users. The MSC Innovation Centre comprises two facilities, namely MSC Lab and Creative Applications & Development Centre (CADC) The MSC Lab contains three components to support and sustain the product innovation life cycle.  The Solution Assessment component (SADC) is a facility open to implementers, user organisations and developers, to minimise technology risks through independent application testing. The Research and Development component enables intellectual property creation through facilitation of R&D activities in the area of Flagship Applications. The Showcase and e-Innovation component aims to encourage wider technology adoption through organised events, workshops and presentations, in addition to providing an exhibition facility to showcase new applications.For more information please contact azlan@mdc.com.my or visit www.mdc.com.my About HP HP is a technology solutions provider to consumers, businesses and institutions globally. The company's offerings span IT infrastructure, personal computing and access devices, global services and imaging and printing. For the fiscal year ending on July 31, 2004, HP revenue totalled US$78.4 billion. More information about HP (NYSE, Nasdaq: HPQ) is available at www.hp.com About Malaysian Genomics Resource Centre Sdn Bhd Malaysian Genomics Resource Centre Sdn Bhd was incorporated on 18th May 2004 with a specific focus of establishing an ASP Bioinformatics service (zoomagene.com, powered by SynaSUITE technologies) for ultra-high-throughput analysis of biological data. The service will be offered on a subscription basis to individual life scientists and researchers worldwide. MGRC will also conduct and publish its own research and collaborate with industry partners on certain projects.  |
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Databases Synamatix stores pattern data 1st June 2004 (Genome Technology) You’ve probably never heard of Synamatix, but that’s no surprise to the people who work for the small database company based in Kuala Lumpur, Malaysia. As Synamatix emerges from stealth mode, it seems to have two main messages: one, that the first product it’s officially launching this August will truly speed up whole-genome comparisons; and two - and perhaps more importantly - that it’s not like the other companies you associate with bioinformatics. With a database that Synamatix refers to as “second generation,” the company itself seems to be looking for recognition as a sort of second generation to the predecessors that failed when the genomics bubble burst. Johan Poole-Johnson, Synamatix’s global marketing manager, says the company started up in 2001 with founder Robert Hercus and has since remained privately funded with some infusion of VC money. The focus is on scoring partnerships to gain credibility: “We are in dealings with some of the genome research institutes,” Poole-Johnson says, and the company has an alliance with Hewlett-Packard as well. The main application, slated to launch this summer, is a structured hierarchical database designed to store many genomes in one repository - Poole-Johnson notes that the goal is to add non-sequence data as well, but that hasn’t been achieved just yet. Zayed Albertyn, senior bioinformaticist at Synamatix, says the database is unique because it “stores information as patterns, based on things like Bayesian statistics.” The database is relational and every bit of information is linked, he adds, so that when a user adds new data, it “will change everything in the database.” The rationale for storing patterns and predictions rather than fixed data, quite bluntly, is for a boost in speed. A project to align and compare sequences between mouse chromosome 11 and human chromosome 17 took “something like three minutes,” says Poole-Johnson, “and we were able to find … homology and even synteny.” Another test run took a comparison that had been run in five hours elsewhere and took just over 500 milliseconds on SynaBase, he adds. Albertyn notes that the speed factor means this database will be targeted at organizations looking into personalized medicine with applications like genotyping whole genomes, such as medical schools or other “institutions that might want to offer high-performance computing solutions.” That said, Poole-Johnson notes that Synamatix isn’t picky about customers. The company will be trying to get its database out to users in pharma and biotech as well. - Meredith W. Salisbury |
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Synamatix Offers Comparative Genomics Shortcut via Pattern-Aware Database 1st June 2004 (Genome Technology) There are generally two ways to speed whole-genome comparisons: faster algorithms or faster hardware. But Synamatix, a bioinformatics startup based in Kuala Lumpur, Malaysia, says it has developed a new approach to this familiar problem that focuses instead on the database that stores the genomic sequence information. This database, called SynaBase, sits at the hub of a suite of products that the company is developing to mine the data stored within it. Johan Poole-Johnson, global marketing manager, said the database relies on pattern-recognition technology that assigns “significance” to certain sequence patterns and then stores the relationships between these patterns. Because the database stores each of these patterns only once, in a hierarchical structure, multiple genomes can be added to the system. These genomes would occupy a much smaller amount of space in SynaBase than they would in relational databases or flat files, which retain redundant information for all the raw sequence data across entire genomes, he said. In addition to the reduced storage requirements, Poole-Johnson said the approach improves upon traditional methods for comparative genomics, which focus on the frequency of certain patterns occurring, rather than their significance. Using the analogy of an English sentence to describe how SynaBase looks at the genetic code, Poole-Johnson said that traditional, similarity-based methods would extract terms like “the,” “an,” and “to,” “because they occur frequently in the language, but they don’t necessarily provide meaning.” SynaBase, by comparison, would be able to hone in on the nouns and verbs that get the speaker’s point across, he said. SynaBase works in concert with SynaSearch and SynaCompare, the company’s genome comparison and visualization tools, to quickly align long genome sequences, and even entire genomes. Synamatix said it has aligned two bacterial genomes in less than 24 seconds, and the human X and Y chromosomes in under 2.5 minutes. A self-comparison of the whole human genome that took 4.5 days to run on a single CPU with Mummer would take only 44 hours using SynaBase, according to the company. Henk Heus, vice president of R&D at Gene-IT and an expert in comparative genomics, said that a new architecture for storing sequences “is a good idea - the result is performance and new science that is not achievable with traditional approaches.” However, Heus noted, from the information that the company has made public about its technology, it’s difficult to assess its accuracy, or how well it is able to “coax syntax and meaning out of the patterns.” According to Poole-Johnson, one demonstration of the company’s technology that proves its pattern-recognition capabilities involves removing all the spaces between the words in a book, and then feeding the book into SynaBase. Once the database identifies the patterns and characters in the book, “we can output those words and their spaces as identical as they were before.” The 15-person company was founded in 2001 by Robert Hercus, the inventor of the pattern-recognition technology that lies at the heart of SynaBase. Hercus has formed several other firms around the same core algorithms, but Synamatix is the first of these to commercialize its technology, Poole-Johnson said. Funded by “a combination of venture capital and angel funding,” Poole-Johnson said that the company has also received a $700,000 grant from the government of Malaysia to develop and commercialize its technology. The company’s product suite will eventually contain at least six additional applications, including SynaMine for sequence analysis, SynaStruct for 2D structural information, and SynaPath for pathway data. - BT Copyright © 2005 GenomeWeb LLC. All Rights Reserved. Be copyright friendly. Would you like to share your online access with your colleagues? For information on an affordable, multi-user site license, contact Allan Nixon. |
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Synamatix Releases
the World’s 1st Ultra High-throughput
Platform for Comparative Whole Multi-Genome Analysis 13 April 2004 Synamatix, a bioinformatics company developing technologies around its proprietary “2nd generation” biological database - SynaBASE, has announced today that it has completed the development of the world’s first high-throughput application for genome to genome comparative analysis. The company is in the process of outlining research and clinical applications for SynaBASE in whole genome genotyping, personalised medicine analysis and true ultra high speed and scale genomics and proteomics. “The performance of our genomics application has even exceeded our own expectations in terms of speed and scalability. We conducted cross species genome analysis using multiple whole genome data sets in milliseconds per query” said Robert Hercus, Founder and Managing Director of Synamatix. “Through utilising our proprietary database, SynaBASE we were able to store genetic data patterns, rather than flat files, in a structured and meaningful form. This not only leads to previously unattainable analysis speeds and data compression, but a unique method for predicting the significance of data. Synamatix is now in partnership and collaboration discussions with key players in the pharmaceutical and biotechnology industries. Its 2nd generation database system has provided a new paradigm for genome and sequence storage and analysis. It is envisaged that SynaBASE’s unique network structure will enable researchers to accelerate and extrapolate qualitative and meaningful results in research areas that were previously out of reach. In total Synamatix has completed development of six analysis tools that integrate with SynaBASE, and has scheduled an additional seven more for development over the next two-year horizon. About Synamatix Synamatix is a 2nd generation bioinformatics company specialising in the creation of databases and research applications for the storage, analysis and mining of genetic sequence data. Since its inception in 2001, Synamatix’s core focus has been to resolve one of the major problems facing the Biotechnology and pharmaceutical industries today i.e. the exponential growth in genomic data continually outpacing advancements in computer processing power and memory. Having created the world’s first integrated structural database system for genetic sequence data, Synamatix is now positioned at the forefront of global bioinformatics database research and development. It is envisaged that Synamatix’s modular suite of applications (SynaSuite) will be able to meet demands placed by scientists at every step in modern, high throughput, functional genomics and proteomics. For more information please email us at  or
alternatively visit our website at www.synamatix.com |
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Aiming for a
Suite Spot Vol. 13 Issue No. 9, 1 August - 10 September 2003 SYNAMATIX. This is the name that is likely to be on everyone's lips come next year. This local company, which is currently developing a special database for use in the life sciences industry, may not be an easily recognised entity among the many IT-related companies in the country. But what it plans to do in the bioinformatics field - should it prove successful - will surely make many sit up and take notice. Maintaining a low profile since its inception in 2002, Synamatix finally announced at a recent joint press conference with Intel and Hewlett-Packard its strategic partnership with HP to ship its flagship genetic sequence database solution, SynaSuite, running on HP's Itanium processor-based servers. While specific details about the product were not revealed due to pending patents, Synamatix's managing director and founder, Robert Hercus nevertheless agreed to an exclusive interview, sharing with Computerworld the company's upcoming plans and reasons for developing the unique database and related suite of applications. Computerworld: Perhaps you could explain what exactly is bioinformatics and why you chose to venture into this field? Robert Hercus: Bioinformatics refers to the use of computer technology to try to understand the patterns of genetic data in the human genome or other organic genomes. We use computer methods to analyse the DNA and try to discover patterns in that data or discover things we never knew about. About two to three years ago, I came across numerous articles about the human genome project on the Internet and that got my interest piqued. The hype was tremendous. Everyone was talking about the possibilities of the human genome being sequenced and the benefits we could reap from them were endless. I researched into it and found an overlapping area in IT where I could put my expertise as an information scientist to good use. That area is bioinformatics and the resulting product was SynaSuite. CW: But how exactly does your product, SynaSuite, fit into this area? Robert Hercus: The key issues that kept on popping up when I was researching into bioinformatics were that existing databases today are not capable of storing the growing volume of genetic data, and the algorithms in finding patterns in genetic data are not capable of extracting meaningful information. (To overcome these issues) you must first understand how genetic sequence data are processed. The raw genetic data are very linear in nature. They consist of a continuous and unsegmented string of text characters that can be up to 3 gigabytes in capacity. To find any sort of pattern that repeats within the data or patterns that can be associated to each other, even other noncontiguous patterns, we have to read the data from the very beginning to the end. Existing databases and algorithms do this at a very time consuming pace and very inefficiently. From my perspective, it's purely a mathematical problem. This is where the idea of SynaSuite originated. SynaSuite provides a structural database of repeating patterns and from that database you can derive meaningful information out of it. SynaSuite also intends to eliminate multiple server farms and consolidate all your resources into one manageable machine or cluster to maximise performance and productivity. CW: But how is this different from a relational database because, essentially, it is still a database that you are developing? Robert Hercus: When you talk about relational databases, you are talking about indexes and key fields that you can index on. But in genetic data, it is just one long continuous string that you can't index on. We are talking purely about representing patterns in data and it doesn't matter whether those data are five characters long or 1,000 characters long. If there are any patterns in that data, we will find them much faster with SynaBase, one of the modules in SynaSuite. SynaSuite was developed to create a more effective database structure for storing genetic data. At the same time, it can also develop more innovative algorithms to find multiple patterns in one processing cycle. CW: Why haven't others thought about this before? Especially major database vendors like IBM or Oracle? Robert Hercus: I'm not saying that other people can't or haven't done it. There might be someone out there trying something similar. But, at the moment and to my knowledge, I'm not aware of anyone trying to do it the way we do. Perhaps it's just not in their interest to do it. All I'm saying is that it's a unique approach. I'm not saying it's an invention or something else. Unfortunately, I cannot disclose how this is done because we are in the process of applying for a patent for our solution that will be out in 18 months. In due time, all will be revealed. CW: During the recent press conference, you mentioned that your products were developed using Microsoft Windows XP, Java and C++. And you are now in the process of converting them for the Linux platform. Could you elaborate on that? Robert Hercus: We are not converting everything for the Linux platform. We are just converting the database backend to Linux. The front end is still Java server-based windows. All our applications are browser-based with applets and Java. Since most genomics companies are running Linux systems, it makes sense to move towards that direction. Portability is another key factor with Linux and Java. All the major hardware vendors like HP, IBM and SGI will have no problems porting our solution to their system as they speak Linux as well. CW: But do you really think Linux is a safe bet? Robert Hercus: Linux has been around for a number of years now. I think it's coming of age if you like. A lot of people are very happy with it. You can play around and do a lot of things with it like Beowulf Clusters and grid computing. All state-of-the-art techniques based on this operating system. I have to admit this is the first time I've ever used Linux. I've been sticking to a single platform all my life. I think if you're planning on sticking to a single platform today, the platform is Linux or open source in general. CW: Who do you think would be interested in your products? And how are you going to market it? Robert Hercus: Our solution will be targeted generally at the life sciences industry and that could include pharmaceuticals, biotechnology companies, or private and public genomics research institutions. Currently, there are no specific marketing strategies but we will draw them up as we progress further ahead. We do expect our business to be coming from mainly offshore. On a side note, we are attending two conferences in partnership with HP. They are the 11th International Conference on Intelligent Systems for Molecular Biology in Brisbane , Australia , and the International Congress of Genetics in Melbourne , Australia . We hope we can generate enough interest and buzz to make all our efforts worthwhile. CW: You probably won't be able to market the product until all the modules within the suite are completed. Or can it be sold separately? Robert Hercus: They can be marketed separately. The core product is SynaBase and SynaSearch. That by itself is sufficient to market the product. SynaCompare adds value. The next two modules - SynaTate and SynaMine - will add even more value and they should be completed by the end of the year. So, our intention is to basically start marketing only next year in January and by then we should have five modules completed. By Blake Hoo Computerworld Malaysia |
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New Structure
for genetic sequence data 28th July 2003 (The Star, Technology, Malaysia) Robert Hercus is the creator of SynaBASE. It is a unique database system that stores and finds patterns in genetic sequence data. The idea to develop SynaBASE came when he retired from the corporate information technology (IT) scene. As he teasingly termed the origin of his idea as "itchy hands", the Australian-born Hercus developed SynaBASE from his home for one year. He went on to form Synamatix Sdn Bhd to develop a suite of tools to be powered by SynaBASE. SynaSUITE, a suite of tools came into the picture. It is designed to overcome the issues plaguing the biotechnology industry such as the rapid growth in sequence data, increasing number of users, storage requirements and processing requirements. If you listen to what he has to say, this is a step change for the life sciences industry. "We took up the challenge two years ago. There were lots of comments in the press, magazines and scientists suggesting that all existing database structures are inadequate for storage and not suitable for the next generation of biology." "Genome data is complex and not easy to represent using relational database model. So, we took this as a challenge, can we design a new database structure that can tackle these issues. You have problems in the rapid growth of genetic sequence data. It is growing sharply and rapidly," he said this during his presentation at the XIX International Genetics Congress in Melbourne earlier this month. Hercus explained that relational databases were not suitable for storing genetic data, which existed in long continuous streams, stretching to over three gigabytes of data per record. "There are no breaks in the stream to segment the data into different fields. Other solutions revert to flat-file searches, whereby the programmes are forced to read data in each record from the beginning to the end. This is very time consuming," he said. No doubt, data is key to researches. Medical scientists and researchers were said to amass and filter data at a rate close to 50 million pages of information a week. Medical scientists face the daunting task of conducting research and development at snail pace due to nagging issues, particularly the lack of data integration and complexity in searching for data due to the enormity in data sizes. As the future of genetics depends primarily on the ability to channel and exploit data and knowledge, it is crucial to have powerful applications that can solve the computational overload issue in the life sciences industry. Synamatix managing director Robert Hercus has been developing SynaSUITE for two years which runs on Linux on a Hewlett-Packard (HP) platform powered by Intel's Itanium 2 processor. SynaSUITE has been designed to analyse series of genomic data faster and more efficiently with significantly less processing power than existing solutions. SynaSUITE is more than speed. Using SynaSEARCH, a search tool, medical researchers would be able to view all the colour-coded sequence patterns, areas of overlap and significant patterns identified in a single search result. Considered as a revolutionary discovery for the life sciences industry, SynaSUITE has attracted HP to partner with Synamatix to strengthen HP's dominance in the information technology (IT) hardware market. Shareholders to Synamatix are local technology venture firm FirstFloor Capital (10% interest), Neuramatix Sdn Bhd (80%) and Labuan-based Encipta Limited (10%), which comes under the Mimos Bhd family. Neuramatix, the developer of the core database technology for SynaSUITE is owned by individual Japanese investors (31%), Encipta Ltd (10%) and Hercus (59%). By Yap Lih Huey |
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HP servers for
genetic solution 17th June 2003 (In.Tech, Malaysia) BIOINFORMATICS pioneer Synamatix Sdn Bhd and Hewlett-Packard have formed a working partnership, offering a combined software and hardware solution that promises to revolutionise the life sciences industry by overcoming critical problems in genetic data management and computational overload. Under the partnership, Synamatix will release its genetic sequence database solution, SynaSuite (which runs on Linux) on Intel Itanium 2-based servers from HP. According the Synamatix, the SynaSuite bioinformatics packages is powerfully efficient, incorporating the world’s first structural database system for genetic sequence data. It has been designed to analyse sequences and other genomic data faster and more efficiently with significantly less processing power than existing solutions. Robert Hercus, managing director of Synamatix said, “To complete applications development and perform benchmarks of SynaSuite, Synamatix needed to invest in a powerful server. HP’s Itanium 2-based server, running Linux, presented the ideal solution for us due to its track record in terms of power, performance and scalability.” “With such a system, Synamatix will be able to not only store whole genomes of various organisms but also facilitate sequence and chromosome comparisons whilst supporting other development functions simultaneously,” he added. Robert was speaking at a joint media briefing by HP and Synamatix announcing the partnership which grew out of a meeting during the BioMalaysia 2002 international biotechnology conference and exhibition. During that event, Synamatix conducted demos of some of the applications in SynaSuite, drawing the attention of various vendors, including some of HP’s life sciences experts. At the media briefing last week, Synamatix was tight-lipped about its database technology as the patents are still pending approval. However, the company disclosed the reasons for its claims to superior performance. “Relational databases (the kind used in every other industry) are not suitable for storing genetic data which exists in long, continuous streams, stretching to over 3GB of data per record,” explained Hercus. “There are no breaks in the stream to segment the data into different fields.” “Other solutions revert to flat-file searches, whereby the programs are forced to read data in each record from the beginning to the end. This is very time consuming,” he added. “We have created a structured database for storing and searching genetic sequence data with near instant access. SynaSuite provides up to a hundred-fold increase in performance compared to existing solutions.” According to Synamatix, while searches using SynaBASE and SynaSearch (SynaSuite’s core applications) are between 50 to 100 times faster than using BLAST by NCBI (the most commonly used search program), the focus is not just on speed. Using SynaSearch, researchers will be able to view all the colour-coded sequence patterns, areas of overlap and significant patterns identified in a single search result. SynaSuite is expected to be available in the local market between the end of this year and early next year. SynaSuite was actually ported from Microsoft’s Windows to a 64bit variant of the Linux operating system. Country business manager for business critical systems, HP Sales Malaysia, Raymond Victor said: “Although a number of operating systems will run on Itanium, HP is partnering with life sciences developers to strengthen the performance of Linux on the new chips. Using Linux, researcher and developers can freely exchange ideas and discoveries about the software with a vast global open-source community.” “Additionally, Linux provides a much lower price tag without any compromise to performance, efficiency and uptime,” he said. By Chris Chong |
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HP
and Intel see potential in the life sciences market
5th June 2003 (The Star, Malaysia) HEWLETT Packard Sales (M) Sdn Bhd and Intel Electronics (M) Sdn Bhd are looking at the US$2.6 billion revenue potential of the Asia Pacific life sciences industry to drive their business growth in the region. Both the major information technology (IT) players are looking at partnerships with life sciences researchers and developers to strengthen the performance of their products. HP country business manager for business critical systems, enterprise systems group Raymond Victor, and Intel Malaysia country manager Peter Choong, expressed optimism on the outlook of the sector at a press conference in Kuala Lumpur yesterday. HP had earlier announced a partnership with local bioinformatics company Synamatix Sdn Bhd (Synamatix), which claimed to have created the world's first bioinformatics software, SynaSuite, running on Linux on an HP platform powered by Intel's Itanium 2 processor. HP and Intel sees the demand for Itanium servers, IT products and chip processors picking up speed as more players enter the biotech industry, which requires super fast computing. International Data Corp (IDC) estimates the Asia Pacific life sciences market to grow at a compounded 46%, with funding injection of US$50bil from both public and private sources. Synamatix managing director Robert Hercus, said he expected SynaSuite to create a "major impact" in the growing biotech industries in Europe , Japan and the US by January next year. Potential clients would include universities, state governments and server providers. "We are in the process of filing our patent," he said, adding that it would take about 18 months to receive the patent. Synamatix will participate at the Genetics Congress in Melbourne in mid July, which would be attended by the who's who in the medical field, including Dr. James Watson, who discovered the structure of DNA. Stakeholders in Synamatix, are Neuramatix Sdn Bhd, 80% interest, and local technology venture firm FirstFloor Capital (10%) and an unnamed offshore company (10%). By Yap Lih Huey |
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Synamatix expects
to market genetic database solution next year 4th June 2003 (Reuters) KUALA LUMPUR, June 4 Synamatix Sdn Bhd, engaged in developing integrated genetic sequence database, expects to market its genetic database solution SynaSuite by January next year. Its managing director, Robert Hercus, told reporters today that the solution, targeted at commercial and academic biotech researchers, has the potential to provide a profound impact on the international life sciences community. "SynaSuite will allow genomics laboratories and researchers worldwide to manage their data effectively, increasing analytical productivity while providing significant savings on data storage," he said. The company today formed a working partnership with Hewlett Packard sales Malaysia Sdn Bhd (HP) to tap into the high growth area of biotechnology. Under the collaboration, Synamatix will ship its SynaSuite, which runs on Linux on the Intel Itanium 2. processor based HP platform. Hercus said that HP's Itanium 2 based server was the ideal solution for the company due to its track record in terms of power, performance and scalability. "With such a system, Synamatix will be able to not only store whole genomes of various organisms but also facilitate sequence and chromosome comparisons whilst supporting other development functions simultaneously," he said. To date, Synamatix has invested RM1 million a year in its research and development division. However, the next investment would see the amount raised to RM2 million, Hercus said. He also said that the company would appoint several agents (apart from HP) to market the SynaSuite solution locally and overseas. "For the first year, we will mainly target on international markets such as research institutions and we expect to appoint several agents in different countries such as the United States, the UK, Europe and Australia and they will represent us to market the product overseas," he said Meanwhile, Country Business Manager for Business Critical Systems, Enterprise Systems Group HP Sales Malaysia, Raymond Victor, said that based on the Linux application, researchers and developers could freely exchange ideas about the software with a vast global open-source community. |