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Distribution by Scientific Domains

Chemistry	50%

Selected Abstracts

TICL , a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics

FEBS JOURNAL, Issue 7 2009
Alexey V. Antonov
High-throughput metabolomics is a dynamically developing technology that enables the mass separation of complex mixtures at very high resolution. Metabolic profiling has begun to be widely used in clinical research to study the molecular mechanisms of complex cell disorders. Similar to transcriptomics, which is capable of detecting genes at differential states, metabolomics is able to deliver a list of compounds differentially present between explored cell physiological conditions. The bioinformatics challenge lies in a statistically valid interpretation of the functional context for identified sets of metabolites. Here, we present TICL, a web tool for the automatic interpretation of lists of compounds. The major advance of TICL is that it not only provides a model of possible compound transformations related to the input list, but also implements a robust statistical framework to estimate the significance of the inferred model. The TICL web tool is freely accessible at http://mips.helmholtz-muenchen.de/proj/cmp. [source]

From Habermas's communicative theory to practice on the internet

INFORMATION SYSTEMS JOURNAL, Issue 4 2003
Michael S. H. Heng
Abstract., Communication plays a crucial role in influencing our social life. However, communication has often been distorted by unequal opportunities to initiate and participate in it. Such conditions have been criticized by Habermas who argues for an ideal speech situation, i.e. a situation of democratic communication with equal opportunities for social actors to communicate in an undistorted manner. This ideal situation is partially being realized by the advent of the internet. The paper describes how an internet-based tool for collaborative authoring was conceptualized, developed and then deployed with Habermas's Critical Social Theory as a guiding principle. The internet-based electronic forum, known by its acronym GRASS (Group Report Authoring Support System), is a web tool supporting the production of concise group reports that give their readers an up-to-date and credible overview of the positions of various stakeholders on a particular issue. Together with people and procedures, it is a comprehensive socio-technical information system that can play a role in resolving societal conflicts. A prototype of GRASS has been used by an environmental group as a new way in which to create a more equal exchange and comparison of ideas among various stakeholders in the debate on genetically modified food. With the widespread use of the internet, such a forum has the potential to become an emergent form of communication for widely dispersed social actors to conduct constructive debate and discussion. The barriers to such a mode of communication still remain , in the form of entrenched power structures, and limitations to human rationality and responsibility. However, we believe that the support provided by the comprehensive system of technological functionality as well as procedural checks and balances provided by GRASS may considerably reduce the impact of these obstacles. In this way, the ideal speech situation may be approximated more closely in reality. [source]

seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments

MOLECULAR ECOLOGY RESOURCES, Issue 1 2010
J-F. FLOT
Abstract The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating phase input files from sequence alignments is an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. During the production of the phase input file, several consistency checks are performed on the dataset and suitable command line options to be used for the actual phase data analysis are suggested. seqphase was written in perl and is freely accessible over the Internet at the address http://www.mnhn.fr/jfflot/seqphase. [source]

Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2010
Salvador Martínez-Bartolomé
Abstract The Human Proteome Organization's Proteomics Standards Initiative aims to develop new standards for data representation and exchange. The Proteomics Standards Initiative has defined the Minimum Information About a Proteomics Experiment (MIAPE) guidelines that specify the information that should be reported with a published experiment. With the aim of promoting the implementation of standard reporting guidelines, we have developed a web tool that helps to generate and store MIAPE compliant reports describing gel electrophoresis and MS-based experiments. The tool can be used in the reviewing phase of the proteomics publication process and can facilitate data interpretation through the comparison of related studies. [source]