SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nucleic acids. In order to increase performance and allow complex analysis with a high degree of abstraction, the relevant (and most frequently queried) data from the MSD is migrated to an object-oriented database developed using the Java Data Objects Technology (JDO). Domain-domain interactions are then determined based on atom-atom distances and the interactions stored. The domain-domain interactions are then classified by family pair and interaction interface and multiple alignments are then generated for each group. SNAPPI-DB contains: (1) Structural information on all (up to a specific date) structures held in the PDB down to the level of atom co-ordinates; (2) Protein Quaternary Structures (PQS) generated structures; (3) ... ... [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]
The primary goal of computational molecular biology, like molecular biology itself, is to understand the meaning of the genomic information and how this information is expressed. We are interested in the problems of predicting biological function of genes and gene products from their primary sequence and structure (sometimes known as functional genomics). We are interested in predicting structure of protein and DNA from its sequence, and understanding how and when genes are expressed. ... [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]
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. [Information of the supplier]
NRCAM, the National Resource for Cell Analysis and Modeling is developing a unique software modeling environment, the Virtual Cell, for quantitative cell biological research. Approaches in computational cell biology are coupled with high resolution light microscopy to facilitate the interplay between experimental manipulation and computational simulation of specific cellular functions that can range from simple molecular motors to tissue-wide process. The Virtual Cell is deployed as a distributed application that is used over the Internet. It is freely accessible to all members of the scientific community. The Virtual Cell has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Likewise the creation of models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Such models can be based on both experimental data and purely theoretical assumptions. ... [Information of the supplier]
