Dataset Information

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

ABSTRACT: With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.

SUBMITTER: Duarte AM

PROVIDER: S-EPMC4477178 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Duarte Afonso M S AM Psomopoulos Fotis E FE Blanchet Christophe C Bonvin Alexandre M J J AM Corpas Manuel M Franc Alain A Jimenez Rafael C RC de Lucas Jesus M JM Nyrönen Tommi T Sipos Gergely G Suhr Stephanie B SB

Frontiers in genetics 20150623

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated ...[more]

PMID: 26157454

Similar Datasets

Project description:BACKGROUND:Every year, the life science field spends billions of dollars on educational activities worldwide. The continuing professional development of employees, especially in this field, encompasses great challenges. Emerging technologies appear to offer opportunity, but relatively little research has been done on the effectiveness of pedagogies and tools that have been used in the life sciences, and even less research has been devoted to understanding the potential power of emerging options that might determine the field's future. OBJECTIVE:In collaboration with the Life Sciences Trainers & Educators Network (LTEN), this study investigated the current state of the pedagogies and tools currently adopted by corporate training professionals in the life sciences as well as the professionals' perceptions of the impacts of emerging technologies on training. METHODS:This study adopted a mixed methods approach that included a survey and a follow-up interview. The survey consists of 18 broad questions with 15 subquestions in each of the five specific sectors of the life sciences field. Interviews were conducted by phone and lasted approximately 40 minutes, covering 18 questions designed to follow-up on findings from the survey items. RESULTS:Both survey and interview results indicated that the professionals were not satisfied with the status quo and that training and education in this field need to change. Most of the techniques and tools currently used have been used for some time. The professionals surveyed were not satisfied with the current techniques and tools and did not find them cost-effective. In addition, the respondents pictured the future of training in this field to be more engaging and effective. CONCLUSIONS:This is the first study in a series designed to better understand education and training in the life sciences on a macro level, in order to build a foundation for progress and evolution of the future landscape. Next steps involve developing strategies for how to extend this vision throughout individual organizations.

Project description:BackgroundDespite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery.MotivationRecent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase.MethodsIn silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures.ResultsOn the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed.ConclusionThe current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.

Project description:BackgroundInformed consent forms for clinical research are several and variable at international, national and local levels. According to the literature, they are often unclear and poorly understood by participants. Within the H2020 project CORBEL-Coordinated Research Infrastructures Building Enduring Life-science Services-clinical researchers, researchers in ethical, social, and legal issues, experts in planning and management of clinical studies, clinicians, researchers in citizen involvement and public engagement worked together to provide a minimum set of requirements for informed consent in clinical studies.MethodsThe template was based on a literature review including systematic reviews and guidelines searched on PubMed, Embase, Cochrane Library, NICE, SIGN, GIN, and Clearinghouse databases, and on comparison of templates gathered through an extensive search on the websites of research institutes, national and international agencies, and international initiatives. We discussed the draft versions step-by-step and then we referred to it as the "matrix" to underline its modular character and indicate that it allows adaptation to the context in which it will be used. The matrix was revised by representatives of two international patient groups.ResultsThe matrix covers the process of ensuring that the appropriate information, context and setting are provided so that the participant can give truly informed consent. It addresses the key topics and proposes wording on how to clarify the meaning of placebo and of non-inferiority studies, the importance of individual participants' data sharing, and the impossibility of knowing in advance how the data might be used in future studies. Finally, it presents general suggestions on wording, format, and length of the information sheet.ConclusionsThe matrix underlines the importance of improving the process of communication, its proper conditions (space, time, setting), and addresses the participants' lack of knowledge on how clinical research is conducted. It can be easily applied to a specific setting and could be a useful tool to identify the appropriate informed consent format for any study. The matrix is mainly intended to support multicentre interventional randomized clinical studies, but several suggestions also apply to non-interventional research.

Dataset Information

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Publications

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets