Our goal: to understand protein folding, misfolding, and related diseases. Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery. Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes. You can help by simply running a piece of software. Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved. We have had several successes. You can read about them on our Science page, on our Awards page, or go directly to our Results page. ... [Information of the supplier, modified]
JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. JSim downloads are available as precompiled binaries (Linux, MacIntosh, Windows) or source code. JSim can also run as an applet within your web browser. JSim is provided free for non-commercial use as a public service by the National Simulation Resource at the University of Washington. ... [Information of the supplier]
Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations. Biodiverse supports four processes: 1. linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2. spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3. spatially constrained agglomerative cluster analyses; and 4. randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface (GUI) and through user written scripts. Currently more than 170 indices are supported. ... [Information of the supplier]
Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized trees (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based. There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, you can upload and display your own trees and data, using the 'Data upload' page or through your personal user account. Use the tabs on the top of the page to navigate or click the trees below to proceed to the interactive pages. Extensive help pages, which provide detailed explanation of iTOL's interface and functions, are available. ... [Information of the supplier]
BioStor provides tools for extracting, annotating, and visualising literature from the Biodiversity Heritage Library (and other sources). It builds on ideas developed for bioGUID (see doi:10.1186/1471-2105-10-S14-S5). The main purpose of BioStor is to find articles in the Biodiversity Heritage Library. To get started you can read the guide to using BioStor, or go directly to the Reference Finder. You can also use BioStor to find references from within EndNote and Zotero. If you use the Firefox web browser you could install the OpenURL Referrer add on, which will add the same functionality to sites that support support COinS, such as Mendeley. ... [Information of the supplier]
SAM is a compact but robust computer program designed as a package of statistical tools for spatial analysis, mainly for applications in Macroecology, Geographical Ecology and Biogeography. SAM offers a wide spectrum of statistical methods used in Surface Pattern Spatial Analysis. It is useful for the studies of spatially distributed biological patterns and processes. There is a Model Selection and Multi-Model Inference module for data exploration and model fitting. Selecting potential explanatory variables, SAM applies Akaike Information Criterion (AIC) to find the most parsimonious linear model. ... [Information of the supplier, modified]
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: 1) Draw pathways with easy to use graphics tools; 2) Color genes on MAPP files based on user-imported genomic data; 3) Query data against MAPPs and the GeneOntology. ... [Information of the supplier]
PlutoF provides cloud database and computing services for the taxonomical, ecological, phylogenetical, etc. research. The purpose of the platform is to provide synergy through common modules for the classifications, taxon names, analytical tools, etc. It allows to address integrated questions in ecology and coevolution of taxa. Different types of the species occurrences, viz. preserved specimens, DNA sequences, human observations, references can be stored in PlutoF as well. PlutoF has no restrictions on taxon and geographic coverage and therefore can be used for the databasing interacting taxa. It includes also collection management module. ... [Information of the supplier]
Use this site to download software based on the maximum-entropy approach for species habitat modeling. This software takes as input a set of layers or environmental variables (such as elevation, precipitation, etc.), as well as a set of georeferenced occurrence locations, and produces a model of the range of the given species. ... [Information of the supplier]
The intention of the GoldenGATE editor is to build a bridge between NLP components and XML markup of natural language text according to arbitrary XML schemas. It allows the deployment of NLP components to marking up the bodies of literature they were designed for. In this way, it enables transforming the texts into XML content according to an XML schema that was designed to gain maximum benefit from the knowledge provided in them. The GoldenGATE editor picks up the ideas of plug-in processing resources and pipelined processing implemented in the GATE framework (http://www.gate.co.uk), which has been widely used in many areas of NLP research. At the same time, it provides a full XML editor including assistance for manipulation of both text and markup, thus allowing users to improve data quality by manual intervention. In order to achieve maximum flexibility and extensibility, the GoldenGATE editor provides plug-and-play interfaces on many levels: Individual automated components for markup creation and manipulation, entire groups of functionalities, components accessing documents in arbitrary storage locations, and arbitrary document data formats. ... [Information of the supplier]
