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Turning data into knowledge  the impacts of bioinformatics
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Turning data into knowledge the impacts of bioinformatics

  1. 8 critical rate-limiting step in genomics is no longer data generation, but rather the speed at which data is remove this rate-limiting step by providing the software platforms for handling large volumes of data. The Bioinformatics Unit focuses on three key areas: (a) the development of an appropriate platform for storage and retrieval of for handling and validating the large volumes of data with special emphasis on data quality; and (c) the development of high-throughput sequence analysis tools and methodologies molecular markers, and as aids to annotation or comparative genomics. All the software development work has been driven by the need to have software packages that do not have operating system or hardware dependencies. Today, the ideal computer languages that implement this approach are Perl or Java, each with their advantages in terms of applications. Database development has largely been in Java, while Perl with its excellent text are called “software pipelines”. The impacts of the Bioinformatics Unit can be demonstrated by these examples of its activities: • Information management systems: The Unit has developed a Laboratory Information Management System (LIMS) that meets the needs of a moderately high-throughput molecular genotyping facility. LIMS sorghum and millet. The application is also being tested for use at the French public institute, CIRAD, and the Brazilian national program, EMBRAPA. The Bioinformatics Unit at CIMMYT – a sister CGIAR center • Data validation and quality: of errors being introduced at various levels of data generation, entry and manipulation. The LIMS helps to reduce these at the data capture point by validating data entry, checking for inconsistencies and possible. A critical next step is often some form of data manipulation. For SSR genotyping using modern DNA sequencers, the manipulation step is to turn a “raw” allele size into its “actual” size – thus allowing more accurate comparisons between varieties to be made. Algorithms that provide a strong statistical basis for these “allele calls” have been implemented into a software package “Allelobin”. The package is available both within the LIMS package, and as a standalone application – ensuring the highest data quality for analysis. Allelobin has been widely distributed at workshops and is being used by scientists Turning Data into Knowledge – The Impacts of Bioinformatics
  2. 9 at CIRAD, IPGRI and Kasetsart University in Thailand. • Sequence analysis tools: When scientists deal with a single DNA sequence or even a few sequences, the desired analyses such as motif searching and primer design are relatively straightforward. It is when dealing with several thousands of sequences, that bioinformatics begins to have an impact. One analysis into single components and identify of the entire process. This may be through building pipelines of software or implementing applications in parallel. Some examples include pipelines of open source software used for putative functional annotation from sequence homology, and parallelized versions of open source multiple alignment and assembly and parsing software, all of which are available as freeware. These tools are now being used extensively by students and scientists at ICRISAT and many other local and international institutes. All have been shared with potential users (eg, CIAT). Parallelized versions implemented on Linux clusters with easy-to-use interfaces have excited interest amongst external users at CIP and CIMMYT. • Strengthening capacity through collaborations: Over the past few years, there has been increased During the last two years, ten graduate students have been accommodated in training programs each year. These students are working towards a degree in biotechnology or bioinformatics and the programs provide them with hands- on training opportunities. In-house capacity is also strengthened through working with collaborators from Central Institutes like the Centre for DNA Fingerprinting and Diagnostics, and the International Institute of Information Technology, both located in Hyderabad. • New linkages with the corporate sector: ICRISAT cannot do it alone. We often seek out consultants and third-parties that can provide the required expertise in bioinformatics. One such company is the Tata Consultancy Services (TCS), a leading global information technology consulting, services and business process outsourcing organization. The Bioinformatics Unit has been working with scientists of the Advanced Technology Centre, the R&D wing for bioinformatics at TCS, to build partnerships in the areas of software platform development, high-throughput comparative biology and systems biology.
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