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THIS RESOURCE IS NO LONGER IN SERVICE. Documetned on May 12,2023. Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

We are principally interested in mechanisms of short-term synaptic plasticity and the impact of that plasticity on function in the nervous system. For our research we use two model vertebrate systems. A simple vertebrate model that affords us some fundamental advantages in this research is the lamprey central nervous system. The lamprey has a central nervous system that is very simple for a vertebrate and which may be kept alive, isolated but otherwise intact, for a number of days. Additionally, a group of axons in the spinal cord are very large and contain presynaptic structures that are exceptionally accessible to the experimentalist. This combination of features enables us to investigate synaptic plasticity at great detail and to determine its role in motor control. We have focused on the means by which G protein coupled receptors mediate enhancement and inhibition of glutamate release. We have identified a direct target for Gbg on the SNARE complex, the machinery for fusion of synaptic vesicles More recently we have utilized the rat hippocampus to determine whether similar mechanisms of synaptic plasticity are present in the mammalian brain. We have begun to focus on the role of kinase activation and short-term modification of transmitter release, in addition to how these modifications can alter the formation of memory during induction phases of long-term plasticity. Available software includes that for Electrophysiological Analysis, Image Analysis, and Confocal Software.

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• SciCrunch
• 15 years ago - by Anonymous

NumPy is the fundamental package needed for scientific computing with Python. It contains among other things: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * tools for integrating C/C and Fortran code * useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Sponsored by ENTHOUGHT

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• SciCrunch
• 17 years ago - by Anonymous

NeuroProSight allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using the Top-Down Approach. This site has many tools and graphical features to facilitate analysis of single (recombinant) proteins, proteins in mixtures, and proteins fragmented in parallel. Sponsors: Dr. John Garavelli is assisting us by incorporating the RESID database of post-translational modifications. We gratefully acknowledge these sources of generous support: * Searle Scholars Program and The Chicago Community Trust * The Burroughs Wellcome Fund * The University of Illinois

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• SciCrunch
• 17 years ago - by Anonymous

A software package for modelling large networks of neurons (typically hundreds or thousands), using spiking point-neuron models. Nengo is designed around the neural engineering framework (NEF). This is a mathematical framework that describes how neurons interact to represent information, perform computations, and behave dynamically. This framework has been used to develop sophisticated models of spatial working memory, probabilistic sound localization, and lamprey locomotion, among others. Nengo makes it easy for beginners to develop models using the NEF. If you accept defaults for spiking models, tuning curves, firing rates, etc. then you can have a rough approximation of a complex system assembled and running in minutes. Nengo also makes it easy for experts to do advanced work with the NEF. The design carefully encapsulates separable aspects of model behaviour, so that it is highly customizable and easy to extend.

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• SciCrunch
• 17 years ago - by Anonymous

Database of long noncoding RNA expression that integrates annotated expression data from various sources in human and mouse. The database contains both microarray and in situ hybridization data, and supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships.

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• SciCrunch
• 17 years ago - by Anonymous

Integrated framework for accessing grid resources that supports scientific exploration, workflow capture and replay, and a dynamic services oriented architecture. This framework provides researchers in the molecular sciences with a tool to discover remote grid application services and compose them as appropriate to the chemical and physical nature of the problem at hand. The initial set of application services include molecular quantum and classical chemistries (GAMESS, APBS, Polyrate), along with supporting services for visualization (QMView), databases, auxillary chemistry services, and documentation and education materials. * Rich-client Desktop Interface - Gemstone is a Firefox extension that provides a dynamic user interface to backend computational, data and visualization services. * Workflow Integration - Gemstone supports a workflow component based on Informnet (see http://grid-devel.sdsc.edu/informnet). They are adapting the Informnet workflow engine to support workflow publication and discovery, brokering, and fault tolerance. They are also adding support for automatic generation of workflows based on user interaction. * Strongy Typed Data Schemas - They are working extensively with CML, integrating their data schemas into workflow systems and providing bridges to the GamesXML that they defined.

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• SciCrunch
• 17 years ago - by Anonymous

motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

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• SciCrunch
• 17 years ago - by Anonymous

ADFS is a web server system that integrates a database of allergenic proteins for food safety. This allergen database for food safety was launched as a project of the Novel Foods and Immunochemistry of National Institute of Health Sciences, and this project was partly supported by a grant from the Ministry of Health, Labor and Welfare. To survey the sequence homology in assessing a potential of allergenicity of a protein in the food, the database has been constructed to include known allergens and B-cell epitope sequences. This database includes 13 (aero animal, aero fungi, aero insect, aero mite, aero plant, contact, food animal, food fungi, food plant, gliadin, protozoan, venom/salivary, and worm) categorized allergens based on allergen type in AllergenOnline, with their accession numbers, epitope information, 3D-structure information, and sugar-containing information . This site also provides sequence search tools for obtaining the sequence homology of a certain protein or peptide relating to allergens (BLAST, epitope(peptide) search). Furthermore, this site provides allergenicity prediction tools of a certain protein (FAO/WHO method, Motif-based method).

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• SciCrunch
• 17 years ago - by Anonymous

A commercial distributed memory object caching system, generic in nature, but originally intended for use in speeding up dynamic web applications by alleviating database load. memcached allows you to take memory from parts of your system where you have more than you need and make it accessible to areas where you have less than you need. With memcached, you can see that all of the servers are looking into the same virtual pool of memory. This means that a given item is always stored and always retrieved from the same location in your entire web cluster.

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• SciCrunch
• 17 years ago - by Anonymous

Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots.

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• SciCrunch
• 13 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

In many respects, this book will be an extension of many of the preoccupations Ive pursued here at Epidemix. Those handful of you who follow my magazine writing will no doubt recognize the theme as well. The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with privacy concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road. Together, these tools will create a new opportunity and a new responsibility for people to act to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways new decision support tools will both inform us and guide us, and theyll be steeped in statistics, predicition, and the power of collective experience.

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• SciCrunch
• 17 years ago - by Anonymous

SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

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• SciCrunch
• 16 years ago - by Anonymous

This portal runs on a processor cluster and allows Biochemists to use our parallel implementation of Clustal W together with our parallel implementation of Minimum Vertex Cover.

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• SciCrunch
• 17 years ago - by Anonymous

Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don''t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Demos here. Gnuplot supports many different types of output: interactive screen terminals (with mouse and hotkey input), direct output to pen plotters or modern printers, and output to many file formats (eps, fig, jpeg, LaTeX, metafont, pbm, pdf, png, postscript, svg, ...). Gnuplot is easily extensible to include new output modes. Recent additions include an interactive terminal based on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element.

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• SciCrunch
• 17 years ago - by Anonymous

The DNA Alignment software and Network software is used by biologists, anthropologists, medical researchers and students world wide. We carry out phylogeographic consultancy for US, UK and German clients, including legal medical work. We were involved in the tv projects The Real Eve (Discovery Channel) and Motherland (BBC). Our biotechnological director Dr Peter Forster is on the editorial board of the International Journal of Legal Medicine since 1999.

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• SciCrunch
• 17 years ago - by Anonymous

Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information.

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• SciCrunch
• 17 years ago - by Anonymous

emPAI (exponentially modified protein abundance index), developed by Ishihama et al., is a measure to describe the protein composition in sample solutions. When the total protein amount in the sample is available, emPAI can be converted to the absolute amount of each protein in the sample. emPAI is derived from PAI, which is defined as the number of the observed peptides divided by the number of the observable peptides per protein. We recently found that log (PAI) had linear relationship to the protein amounts, and that emPAI, 10^(PAI)-1, was proportional to the protein amounts for whole cell lysate digested by trypsin. The accuracy of this method was within factor 5, similar or better than determination of abundance by protein staining

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database which contains the information of heparin-binding proteins of E. coli K-12 MG1655 cells. Heparin affinity columns were applied to enrich and fractionate proteins. Identification of proteins was done via the collaboration with David Russell''s lab. Because heparin is negatively charged sulfated glucosaminoglycan, polyamion binding proteins, which contain nucleic acid-binding proteins, are expected to bind to heparin columns. Study of the expression pattern of heparin-binding proteins will help to study the nucleic acid-binding proteins, most of which are related to regulation. Moreover, heparin affinity columns will also erich low abundance proteins. Heparome database is constructed using MySQL. Website interface is built using HTML and PHP. Queries between MySQL database and website interface are executed using PHP. Besides including information of identified proteins, such as swiss accession number, gene name, molecular weight, isoelectric point, condon adaptation index (CAI), functional classification, et. al. , it also includes information of experiments, such as sample preparation, heparin-HPLC chromatography, SDS-PAGE gel separation and MALDI-MS.

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• SciCrunch
• 17 years ago - by Anonymous