Bioinformatics: Encyclopedia - Bioinformatics Bioinformatics or Computational Biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution. The terms bioinformatics and computa ..
Working binaries with menus -- good for Suse 11.1 I have built Linux binaries of molmol 2K-2 on RH v7.3 and RH v9. You can obtain these here but I cannot guarentee these will work for you. I do not have stock RH 7.3 or RH 9 distributions for software compilation because I regularly update these systems with apt-get (the RH version, natch).
Biomedical research is benefiting from the wealth of new data generated in the laboratory through new instrumentation, greater computational resources, and massive repositories of public domain data. Using these data to make scientific discoveries is sometimes straightforward, but can be complicated by the number and breadth of public sources available to the researcher as well as by the plethora of tools from which to choose. These articles aim to explain how to set up and administrate Core Facilities, and the benefits to researchers and institutions of so doing.
The backbone of the free DICOM Visualization and Analysis tool SMIViewer has been released as SMISDK. SMIViewer has developed a respectable following among radiology and biomedical experts, and the release of the SDK is the first step to releasing SMIViewer under a similar GPL license. The project team, “pixel.to.life” and Prashant Chopra, have this to say:
Using classic hologram imaging techniques, researchers at New York University have created a “holographic microscope” capable of visualizing individual biological molecules with amazing precision.
In 2007, the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico, best known for the development of bioinformatics tools, established the Schizophrenia Genome Project. Taking Illumina GA sequence data, NCGR scientists used a combination of homegrown Alpheus software and JMP Genomics (from SAS) to develop a streamlined workflow for the acquisition, analysis, and management of huge amounts of next-generation sequencing data—in this case, mRNA.
Last year, researchers at Indiana University's Cryo-Transmission Electron Microscopy Facility (cryoEM) acquired a powerful new microscope capable of electron cryomicroscopy, a method of analyzing the structure of proteins at really low temperatures. However, the process often damages samples so researchers have to use a large number to ensure accurate results. This in turn means multiple images from hundreds of thousands of protein particles which then need to be made into composite images, requiring thousands of hours of compute time. So the analysis, movement, and management of all these image files quickly became an IT headache almost as soon as they flipped the on switch
visual guide to Circos A visual guide to Circos (Circos - an information aesthetic for comparative genomics) presents some of the capabilities of Circos and illustrates its application in the field of comparative genomics and genome visualization.
World Index of BioMolecular Visualization Resources Free Molecular Visualization and Modeling Software Caution: Some of free software listed here is Open Source in the strict sense, meaning that all derivatives are required to be free with open source code. If you plan to use the source code (not just the executable program), read the copyright restrictions carefully.
The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.
The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.
Yesterday I gave a talk to the Informatics group at the Wellcome Trust Sanger Institute that focused on using Cloud computing within a scientific domain.
The Theoretical and Computational Biophysics Group is a pioneer in the realm of high-performance computing. To meet our computational needs, we maintain a wide selection of computers divided into four main categories: compute power, visualization equipmen
Cyberinfrastructure makes the development and deployment of bioinformatics applications easier by providing the framework and components that may be loosely coupled using service oriented architecture. Here we describe an end to end prototype environment
A privately financed team of scientists and engineers is nearing completion of a special-purpose supercomputer intended to offer more than a thousandfold increase in performance for complex molecular simulations.
SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast