Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

Abstract

SUMMARYThe topic 'Portals for life sciences' includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user's interaction with computational resources that are concerted to a supported application domain. Copyright ᭧ 2010 John Wiley & Sons, Ltd. IWPLS'09It is our great pleasure to introduce this special issue on the First International Workshop on Portals for Life Sciences held at the e-Science Institute in Edinburgh, U.K., on 14-15 September 2009. The workshop was focused on research contributions for portals and tools in the field of life sciences and brought together scientists from the fields of life science, bioinformatics, and computer science. It formed an international platform to exchange experience, formulate ideas, and catch up on technological advances in molecular and systems biology in the context of portals. The variety of nationalities covered by the delegates reflects the international interest in a platform on scientific portals. Delegates from Austria, Brazil, Germany, Hungary, Italy, The Netherlands, Norway, Spain, The United Kingdom and The United States of America contributed to and attended the workshop. We especially highlight the mix of technology-related and domain-related talks, which mirrors the diverse scientific background of the delegates.Papers and abstracts for the workshop were accepted through a blind peer-reviewing process. Accepted papers resulted in 30-min presentations and were published in an open-access workshop proceedings. Accepted abstracts resulted in a 10-min 'lightning talk'. The speakers gave excellent and thought-provoking presentations. The highlights were presentations from two invited keynote speakers. In addition to the presentations, lively and promising discussions took place after talks, in coffee breaks and even during the social event. The workshop was highly successful and turned out to be the starting point of an international workshop series with the subject extended to science gateways for e-Science: The International Workshop on Science Gateways.We faced the challenge to invite several authors for extended versions of their papers and abstracts for this special issue. Some of the papers in this special edition are combinations of papers * Correspondence to: Sandra Gesing,

A new optimization phase for scientific workflow management systems

“…Although, many design frameworks [35] have been developed, they are not accessible for scientists working with scientific workflows and workflow management systems. Instead, parameter sweeps and manual trial and error are still the methods of choice for life science researcher today [36,37], which was therefore used as comparison here. To our knowledge there is no other comprehensive approach for general workflow optimization freely available today, except Nimrod/OK [7], which is a more specialized workflow parameter optimization tool from the engineering domain and apparently not available for download.…”

Science Gateway Canvas

“…It discusses three-versus four-tier patterns for SG system architecture, and reviews a few tools and frameworks that can be used to combine Web and grids. Gesing et al [10] present and compare SG functionalities for Life Sciences applications. The categories used for comparison cover a subset of the function groups of our reference model, mostly focusing on management of grid computation, data and security.…”

Parallel image sharpness measure for supercomputing environment

“…There are numerous possibilities as multiple eScience gateway platforms are available, for example the MOSGrid portal [1,2] or ProGenGrid [3], or the High-Performance Computing Infrastructure for South East Europe (HPSEE) project [4].…”