Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
Grid computing is the use of widely distributed computer resources to reach a common goal. A computing grid can be thought of as a distributed system with non-interactive workloads that involve many files. Grid computing is distinguished from conventional high-performance computing systems such as cluster computing in that grid computers have each node set to perform a different task/application. Grid computers also tend to be more heterogeneous and geographically dispersed than cluster computers. Although a single grid can be dedicated to a particular application, commonly a grid is used for a variety of purposes. Grids are often constructed with general-purpose grid middleware software libraries. Grid sizes can be quite large.
E-Science or eScience is computationally intensive science that is carried out in highly distributed network environments, or science that uses immense data sets that require grid computing; the term sometimes includes technologies that enable distributed collaboration, such as the Access Grid. The term was created by John Taylor, the Director General of the United Kingdom's Office of Science and Technology in 1999 and was used to describe a large funding initiative starting in November 2000. E-science has been more broadly interpreted since then, as "the application of computer technology to the undertaking of modern scientific investigation, including the preparation, experimentation, data collection, results dissemination, and long-term storage and accessibility of all materials generated through the scientific process. These may include data modeling and analysis, electronic/digitized laboratory notebooks, raw and fitted data sets, manuscript production and draft versions, pre-prints, and print and/or electronic publications." In 2014, IEEE eScience Conference Series condensed the definition to "eScience promotes innovation in collaborative, computationally- or data-intensive research across all disciplines, throughout the research lifecycle" in one of the working definitions used by the organizers. E-science encompasses "what is often referred to as big data [which] has revolutionized science... [such as] the Large Hadron Collider (LHC) at CERN... [that] generates around 780 terabytes per year... highly data intensive modern fields of science...that generate large amounts of E-science data include: computational biology, bioinformatics, genomics" and the human digital footprint for the social sciences.
Erik Bongcam-Rudloff is a Chilean-born Swedish biologist and computer scientist. He received his doctorate in medical sciences from Uppsala University in 1994. He is Professor of Bioinformatics and the head of SLU-Global Bioinformatics Centre at the Swedish University of Agricultural Sciences. His main research deals with development of bioinformatics solutions for the Life Sciences community.
The cancer Biomedical Informatics Grid (caBIG) was a US government program to develop an open-source, open access information network called caGrid for secure data exchange on cancer research. The initiative was developed by the National Cancer Institute and was maintained by the Center for Biomedical Informatics and Information Technology (CBIIT) and program managed by Booz Allen Hamilton. In 2011 a report on caBIG raised significant questions about effectiveness and oversight, and its budget and scope were significantly trimmed. In May 2012, the National Cancer Informatics Program (NCIP) was created as caBIG's successor program.
Advanced Resource Connector (ARC) is a grid computing middleware introduced by NorduGrid. It provides a common interface for submission of computational tasks to different distributed computing systems and thus can enable grid infrastructures of varying size and complexity. The set of services and utilities providing the interface is known as ARC Computing Element (ARC-CE). ARC-CE functionality includes data staging and caching, developed in order to support data-intensive distributed computing. ARC is an open source software distributed under the Apache License 2.0.
European Grid Infrastructure (EGI) is a series of efforts to provide access to high-throughput computing resources across Europe using grid computing techniques. The EGI links centres in different European countries to support international research in many scientific disciplines. Following a series of research projects such as DataGrid and Enabling Grids for E-sciencE, the EGI Foundation was formed in 2010 to sustain the services of EGI.
The D-Grid Initiative was a government project to fund computer infrastructure for education and research (e-Science) in Germany. It uses the term grid computing. D-Grid started September 1, 2005 with six community projects and an integration project (DGI) as well as several partner projects.
Carole Anne Goble, is a British academic who is Professor of Computer Science at the University of Manchester. She is principal investigator (PI) of the myGrid, BioCatalogue and myExperiment projects and co-leads the Information Management Group (IMG) with Norman Paton.
The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of e-laboratories and have been used in domains as diverse as systems biology, social science, music, astronomy, multimedia and chemistry.
Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). MGI provides access to data on the genetics, genomics and biology of the laboratory mouse to facilitate the study of human health and disease. The database integrates multiple projects, with the two largest contributions coming from the Mouse Genome Database and Mouse Gene Expression Database (GXD). As of 2018, MGI contains data curated from over 230,000 publications.
Physiomics is a systematic study of physiome in biology. Physiomics employs bioinformatics to construct networks of physiological features that are associated with genes, proteins and their networks. A few of the methods for determining individual relationships between the DNA sequence and physiological function include metabolic pathway engineering and RNAi analysis. The relationships derived from methods such as these are organized and processed computationally to form distinct networks. Computer models use these experimentally determined networks to develop further predictions of gene function.
Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.
Discovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services standards. The system was designed and implemented at Imperial College London as part of the Discovery Net pilot project funded by the UK e-Science Programme. Many of the concepts pioneered by Discovery Net have been later incorporated into a variety of other scientific workflow systems.
AstridBio Ltd. is a privately held Biotechnology company with office in Hungary. AstridBio's focus is biobanking software development, data management and analysis for genomics research. Its clients include academic research institutes, pharmaceutical and biotech companies.
The iPlant Collaborative, renamed Cyverse in 2017, is a virtual organization created by a cooperative agreement funded by the US National Science Foundation (NSF) to create cyberinfrastructure for the plant sciences (botany). The NSF compared cyberinfrastructure to physical infrastructure, "... the distributed computer, information and communication technologies combined with the personnel and integrating components that provide a long-term platform to empower the modern scientific research endeavor". In September 2013 it was announced that the National Science Foundation had renewed iPlant's funding for a second 5-year term with an expansion of scope to all non-human life science research.
Integromics was a global bioinformatics company headquartered in Granada, Spain, with a second office in Madrid, subsidiaries in the United States and United Kingdom, and distributors in 10 countries. Integromics specialised in bioinformatics software for data management and data analysis in genomics and proteomics. The company provided a line of products that serve the gene expression, sequencing, and proteomics markets. Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations, and biotechnology companies.
In silico medicine is the application of in silico research to problems involving health and medicine. It is the direct use of computer simulation in the diagnosis, treatment, or prevention of a disease. More specifically, in silico medicine is characterized by modeling, simulation, and visualization of biological and medical processes in computers with the goal of simulating real biological processes in a virtual environment.
The Centre for Genomic Regulation is a biomedical and genomics research centre based on Barcelona. Most of its facilities and laboratories are located in the Barcelona Biomedical Research Park, in front of Somorrostro beach.
The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure initiated by the Federal Ministry of Education and Research funding 2015-2021. The network provides bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data. From 2022, the network will be integrated into Forschungszentrum Jülich.
