new on the market The breakdown on bioinformatics Hardware and software make up this survey — items include software for genomics work, DNA and protein sequence analysis, protein viewing, and a number of products for drug discovery and drug screening applications.
Bioinformatics Workbench tation of thousands of sequences. Once From MDL Information Systems defined, these strategies can be saved and used for subsequent analyses, standardizing An intranet-based ‘virtual laboratory’ that and distributing bioinformatics information delivers data and computing tools for throughout the user’s organization. By select- genomic research ing analysis steps from pull-down menus, Developed at the National Center for customers can define strategies for automat- Supercomputing Applications (NCSA) at ed gene finding, domain finding, functional the University of Illinois, the Bioinformatics identification, EST analysis and secondary Workbench provides an environment that structure prediction. A technology agree- integrates the genome-related tools and ment with Paracel enables customers to databases emanating from sequencing include accelerated Smith–Waterman, pair- efforts on many plant and animal species. wise alignment analyses in their strategies This system is designed to tie together soft- Incyte Pharmaceuticals’ LifeTools 3D software. Reader Enquiry No. 103 ware that is already available. Workbench offers a platform-independent interface to collaboration with Silicon Graphics, the com- Gene Explorer more than 100 public domain databases pany has created customized functions that From MSI and software packages for DNA and pro- are designed to help explore LifeSeq, includ- A new computational environment for the tein sequence analysis. With this software, ing Protein Function Hierarchy Visualization, analysis of DNA and protein sequences, as scientists connect via a Web browser on which displays the relative expression of genes well as protein structures their corporate intranets to search all across tissues. There is also MultiGene major molecular and structural biology northern visualization, which uses a three- From restriction analysis to virtual site- databases. The Bioinformatics Workbench dimensional graph to show the tissue distrib- directed mutagenesis, Gene Explorer strives uses a generic design that allows tools, ution for a selected set of genes. This to meet the computational needs of molecu- databases, servers and computer engines program is a UNIX-based, client/server lar biology researchers within a single envi- based on different formats to interoperate. application, requiring Mineset 1.1 (offered ronment. It should help to focus the user’s The interface to these components works by the company with LifeTools 3D). research on the most promising leads, with any standard forms-capable, HTML Reader Enquiry No. 101 hypotheses and candidate genes. In a series of browser. Previously known as Biology steps, 3D Structure Prediction will transform Workbench, the program was developed MM3 Software protein sequence into a three-dimensional by the Computational Biology Group of From Tripos structure model, search databases for similar the NCSA. The NCSA version is available solved protein structures, present search The 1996 version of the company’s molecular free to the academic community at results in a graphical display of homology, mechanics software
NATURE VOL 388 7 AUGUST 1997 | | Nature © Macmillan Publishers Ltd 1997 603 new on the market ing pockets of related proteins. The initial million affine SW cells per second. Users tions, such as real-time, three-dimensional release included generalized valence bond can reorganize the cluster for rapid interac- volume roaming. (GVB) theory, which incorporated the tive results, while production searches are Reader Enquiry No. 107 pseudospectral (PS) numerical methods for streamed as a batch-mode, background fast evaluation of the two-electron integrals. process as resources become available. A More software Over the last three years, however, the prod- simple, automatic script-based, semaphore Synergy uct has outgrown its name in terms of func- mechanism pauses each CPU, permitting From NetGenics tionalities and capabilities. periodic database updates to be cloned An alliance with Incyte Pharmaceuticals will Reader Enquiry No. 105 across the cluster without loss of queued link Synergy and Incyte’s genomic database search requests or results. By using standard software Hardware systems Intel technology with Windows-NT, the DeCypher II cost of ownership is lowered. Synergy assists in the drug discovery process From Time Logic Reader Enquiry No. 106 by enhancing the researcher’s ability to access and analyse biological information. Incyte A system designed to provide the will incorporate certain aspects of NetGenics’ infrastructure to handle large-scale DNA Octane workstations software and the CORBA (common object sequence comparison analysis From Silicon Graphics request broker architecture) framework into A new line that features high-performance The ultra-high performance cluster of its database products and the companies will graphics, symmetric multiprocessing and a this sequence similarity search system jointly develop a product that is designed to pure 64-bit computing environment should help to identify rapidly similar provide increased functionality to Incyte’s sequences and deliver results quickly to the Octane workstations are said to have database and software subscribers by facili- geneticist. The system’s logic circuit adapts improved systems and I/O bandwidth, giv- tating project management and allowing the to additional algorithms through software ing greater flexibility to expand their applica- integration and query of multiple, unrelated reconfiguration, eliminating hardware tions. The system shares many components relational databases. Synergy is a cross-plat- obsolescence associated with older tech- with the company’s supercomputing archi- form, client/server-based bioinformatics nologies. System specifications include tecture, employing a unique seven-port computer software system. It parallels the 1.5–12 billion affine SW cells per second crossbar switch in lieu of the conventional organization of multidisciplinary drug teams per rack, 1–8 15-accelerator systems per shared bus architecture. It also combines this and enables the members of a drug team to 48-cm rack, Xilinx reconfigurable compu- high-bandwidth switch with single or dual communicate efficiently. tational arrays, 1–8 single- or dual-SMP MIPS R10000 processors and fast desktop Reader Enquiry No. 108 Pentium CPUs, a Windows-NT TCP/IP graphics. Furthermore, it is said to offer a network server, cluster scalability and a 70 per cent increase in floating-point Diva and RS3 Discovery 32–144 GB hard-drive capacity per rack. performance over the Indigo2 Impact 10000 From Oxford Molecular CPU clusters offer high Smith–Waterman family. With a peak bandwidth of 1.6 GB s11 Six products designed to increase the speed throughput, starting with a single 15-accel- per port, the seven-port crossbar switch is and efficiency of the drug discovery process erator system. Each rack expands to hold up stated to provide as much as 210 times the to eight systems, for a total of 120 Similarity bandwidth found in traditional architec- These software packages add some 25 soft- Engine accelerators at a stated 12 billion tures. The system is designed to process mul- ware tools for use in academic research and affine SW cells per second. Special fault- tiple data types, including audio, video, the pharmaceutical, chemical and biotech- tolerant versions are also available. The imagery and three-dimensional geometry. nology industries. Each product — Diva, company offers custom hardware and soft- With hardware-accelerated geometry pro- CAChe 3.0, Tsar 3.0, Topkat 5.0, UniChem ware development and support. According cessing and high-speed texturing and image 4.0 and RS3 Discovery — deals with a differ- to the manufacturer, virtually unlimited processing, Octane systems enable real-time ent aspect of the process of drug discovery; scalability is achieved by partitioning the visual imagery for applications ranging from taken together, they should help scientists query stream across one or more racks. solid modelling, defence imaging, three- predict the properties and toxicities of drug Each 15-card CPU contributes up to 1,500 dimensional animation and emerging solu- candidates and enable comparisons with
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NATURE VOL 388 7 AUGUST 1997 604 Nature © Macmillan Publishers Ltd 1997 | | new on the market chemicals in existing databases. Diva was applications — TIFF images may be created to allow researchers to mine corpo- imported or exported. Images and rate databases and identify the properties sequences can be printed on any standard and relationships of thousands of com- printer as they are or with lanes, band labels pounds. Version 3.0 of CAChe allows exper- and annotation. imental chemists to predict and analyse Reader Enquiry No. 110 properties of drug candidates and chemicals on a PC. Tsar 3.0 was written to help identify Antisense Functional Genomics structure–activity relationships quickly by From Sequitur integrating QSAR data, computations and The commercial availability of statistics into one package. Topkat, now in second-generation antisense compounds version 5.0, offers a Windows environment and focuses experimental testing by quickly extendLRS sequencing software from Genomyx. These compounds have been developed and accurately assessing the toxicity of drug through careful screening in a cell culture candidates based on structure. UniChem images obtained from the Genomyx SC flu- assay system. With this program, the optimizes chemical reactions with property orescent imaging system. It also processes company does not retain the rights to predictions that should aid in the design of images from other sources, including the research findings derived through catalysts and in the prediction of reaction autorads and images as large as 50 Mb. This their use. mechanisms. Lastly, RS3 Discovery uses Ora- system includes the company’s automatic Advantages of these compounds are cle to store and retrieve information in a band detecting and labelling, and lane said to include improved specificity and flexible open architecture. tracking technology. reduced toxicity, target gene inhibition Reader Enquiry No. 109 By eliminating manual calculations and with only three to six compounds guesswork, extendLRS increases base-call- screened, as well as rapid and cost-effective extendLRS ing accuracy, says Genomyx. The new soft- results, according to Sequitur. From Genomyx ware can read sequences as long as 400 Reader Enquiry No. 111 bases with a high degree of accuracy. Several Software for automated DNA sequencing and software tools are included for stepping These notes are compiled by Brendan Horton analysis through and editing the sequence. DNA from information provided by the manufacturers. The extendLRS sequencing software has sequence information can be exported in For more details, fill in the reader service card been designed primarily for the analysis of ASCI text or SCF format for use in other bound inside the journal.
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NATURE VOL 388 7 AUGUST 1997 | | Nature © Macmillan Publishers Ltd 1997 605