Identification of epitopes which invoke strong humoral responses is an essential issue in the field of immunology. Localizing epitopes by experimental methods is expensive in terms of time, cost, and effort; therefore, computational methods feature for its low cost and high speed was employed to predict B-cell epitopes. In this paper, we review the recent advance of bioinformatics resources and...

Being a relatively new addition to the 'omics' field, metabolomics is still evolving its own computational infrastructure and assessing its own computational needs. Due to its strong emphasis on chemical information and because of the importance of linking that chemical data to biological consequences, metabolomics must combine elements of traditional bioinformatics with traditional cheminforma...

A framework for expression data repositories (MAGE-ML compatiblity) emerged during the last years. Focus is now shifting towards the integration of expression databases into genomic and other bioinformatic database system as well as with statistical analysis platforms. We present an implementation of such a repository system at MIPS (http://mips.gsf.de/). An important requirement for this integ...

Because the label "computing and philosophy" can seem like an ad hoc attempt to tie computing to philosophy, it is important to explain why it is not, what it studies (or does) and how it differs from research in, say, "computing and history," or "computing and biology". The American Association for History and Computing is "dedicated to the reasonable and productive marriage of history and com...

Signal transduction is a fundamental process that takes place in all living organisms and understanding how this event occurs at the cellular level is of vital importance to virtually all fields of biomedicine. There are several major steps involved in deciphering the signalling pathways: (a) Which molecules are involved in signalling? (b) Who talks to whom?, ie making sense of the molecular in...

Medical informatics has shifted its focus from acquisition and storage of healthcare data by integrating computational, informational, cognitive and organisational sciences to semantic analysis of the data for problem solving and clinical decision-making. In this transition, bioinformatics tools and resources are the most appropriate means to improve the analysis, as major biological databases ...

Huge volume of biological data, which is heterogeneous, autonomous and dynamic in nature, is being produced at a rapid pace throughout the community. Along with the increase in biological data, many tools are being designed to analyze them by different research groups. Integration of these biological data and tools is becoming one of the major topics in the bioinformatics community. Grid comput...

The fast growth of biological databases has attracted the attention of computer scientists calling for greater efforts to improve computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multicore processors. Here we present a preliminary study of the Cell BE limitations when executing a representativ...

Databases are integral part of bioinformatics and need to be accessed most frequently, thus downloading and updating them on a regular basis is very critical. The establishment of bioinformatics research facility is a challenge for developing countries as they suffer from inherent low-bandwidth and unreliable internet connections. Therefore, the identification of techniques supporting download ...

MOTIVATION The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML ...