Curator Dashboard

It provides quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae). PROPHECY evalutes the phenotype of a deletion strain on the basis of growth behaviour during micro-cultivation. PROPHECY quantifies growth aberrations by estimating the rate of growth, the efficiency of growth and the adaptation time.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

This portal takes you to the website of Professor Anne Chao of the National Tsing Hua University, China. She studies birds. The portal offers Software, course information, publications and teaching. There are about 458 bird species in Taiwan. We have observed 155 species in our neighboring Ker-Yar estuary. We would estimate the total number of species in this area to be 180 including those unobserved. The more we discover about birds, the more we realize how intimately and closely our lives are entwined with those of birds. When the habitats of birds are destroyed and birds become extinct, we human beings are losing the land....

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Our research group develops and applies computational techniques for modeling and understanding biological processes at the molecular level. Our research emphasizes the application of statistical and machine learning techniques, such as hidden Markov models and support vector machines. We apply these techniques to various types of biological data, including DNA and protein sequence data, as well as gene expression data from microarray experiments. We are currently developing methods for analyzing shotgun proteomics data, for characterizing protein function, structure and interactions, and for understanding the structure and regulatory influence of chromatin.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Their primary focus is in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 Centers each lead by a Center Leader and a senior Manager (BAC Library Construction Center, BAC/EST Resource Center, Sequencing & Physical Mapping Center (including: production sequencing and fingerprinting, and sequence finishing), Bioinformatics Center and the Evolutionary and Functional Genomics Center). AGI is housed in the state of the art Thomas W. Keating Bioresearch Building on the northeast part of campus near the Medical School. AGI currently employees about 30 scientists and is primarily funded through federal grants, private contracts, and the Bud Antle Endowed Chair in Plant Molecular Genetics. Sponsors: AGI is supported by Bio5, Plant Sciences, National Science Foundation, National Institues oh Health, and USDA.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Family Pairwise Search (FPS) is a protein homology detection algorithm that combines sequence similarity scores from a pairwise alignment algorithm such as Smith-Waterman or BLAST. Source code and a web server are available. This is a method for scoring a query sequence against a family of sequences. (Note: the query sequence may alternatively be a sequence, a GCG profile or a BLAST checkpoint file.) FPS compares the query sequence individually (pairwise) to each sequence in the family and then combines the pairwise scores into an overall score for the match. This site provides access to * a web server to allow you to use FPS to search various protein family libraries for matches to a protein sequence, * an overview of the FPS algorithm, * a description of the inputs and outputs for the FPS server, * a sample output from the FPS server, and * a release notes for FPS, and * links to several papers about FPS, and * the FPS source code for non-comercial use. * COPYRIGHT information and how to license FPS for commercial use is described here.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Arizona CERT is an independent research and education center whose mission is to improve therapeutic outcomes and reduce adverse events caused by drug interactions and drugs that prolong the QT interval, especially those affecting women. The CERTs mission is to conduct research and provide education that will advance the optimal use of drugs, medical devices, and biological products The Arizona CERT is a program of the Critical Path Institute in collaboration with the Center for Health Outcomes and PharmacoEconomic Research at The University of Arizona College of Pharmacy. It is one of 14 national CERTs funded by the U.S. Agency for Healthcare Research and Quality (AHRQ).

• Resource
• SciCrunch
• 17 years ago - by Anonymous

This is a Research Community that is focused on reducing the threat of the Aspergillus flavus fungus and its toxin to human and animal health. Aspergillus flavus is a plant, animal, and human pathogen that produces the carcinogen, aflatoxin. An organized multidisciplinary team is coordinating research efforts to control this fungus and to prevent the formation of its toxin in food and feeds. Aspergillus flavus is a fungus. It grows by producing thread like branching filaments known as hyphae. Filamentous fungi such as A. flavus are sometimes called molds. A network of hyphae known as the mycelium secretes enzymes that break down complex food sources. The resulting small molecules are absorbed by the myceilium to fuel additional fungal growth. The unaided eye cannot see individual hyphae, but dense mats of mycelium with conidia (asexual spores) often can be seen. The ear of maize below shows the growth of the fungus covering four maize kernels. When young, the conidia of A. flavus appear yellow green in color. As the fungus ages the spores turn a darker green. Sponsors: This resource is supported by the Center for Integrated Fungal Research. Keywords: Aspergillus flavus, Research, Fungus, Toxin, Human, Animal, Health, Plant, Pathogen, Carcinogen, Aflatoxin, Food, Feed, Mold, Network, Enzyme,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Audacity is free, open source software for recording and editing sounds. It is available for Mac OS X, Microsoft Windows, GNU/Linux, and other operating systems. The latest release of Audacity is 1.3.12 (Beta). This is their active work in progress version with their latest features. Documentation and translations into different languages are not quite complete. They recommend this version for more advanced users, and for everyone on Windows 7, Windows Vista and Mac OS X 10.6. See New Features in 1.3 for more information about the 1.3 Beta series. You can use Audacity to: Convert tapes and records into digital recordings or CDs. Edit Ogg Vorbis, MP3, WAV or AIFF sound files. Cut, copy, splice or mix sounds together. Change the speed or pitch of a recording. And more See the complete list of features. Sponsors: This resource is supported by UmixIt Technologies, LLC. Keywords: Software, Recording, Audio, Sound, Editor, Recorder,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

The fairly common occurrence of hearing-loss or deafness in both humans and mice, and the anatomical and functional similarities of their inner ears, attest to the potential of mice as models to study hereditary hearing loss. Hundreds of standard inbred, recombinant inbred, and congenic strains are maintained at The Jackson Laboratory, as well as hundreds of inbred strains with spontaneous or induced mutations. To assess hearing impairment in inbred and mutant strains of mice we measure auditory-evoked brainstem response (ABR) thresholds.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan).

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A web interface for identification of potential inter-species CNV information by finding duplicated regions within a genome (paralogues) and between different genomes (orthologues). The paralogues/orthologues are inferred from pairwise sequence alignments between 16 vertebrate species. Note that the CNVs referred here are not equal to copy number polymorphisms of a population. Further experimental evidence is needed to support the polymorphism status of the inferred CNVs in this database.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe. The collection is part of Ghent University. Keywords: Bacteria, Plasmid, DNA, Library, Collection, Microbiology, Molecular biology, Biology,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Gist contains software tools for support vector machine classification and for kernel principal components analysis. The SVM portion of Gist is available via an interactive web server. The Gist package contains the following programs: * gist-train-svm trains a support vector machine based upon a given set of labeled training examples, permitting feature selection and leave-one-out cross-validation, * gist-classify applies a trained support vector machine to unlabeled data to produce predicted binary classifications. * gist-fast-classify does the same thing as gist-classify, but uses less time and memory. However, this program only works in conjunction with a linear kernel function. * gist-kpca performs kernel principal components analysis on a given data set, and * gist-project projects a data set onto the components discovered by gist-kpca. In addition to the primary programs, the following auxiliary programs are included: * gist-fselect performs linear feature selection on a given data set, using binary classification labels, * gist-matrix performs basic manipulations of matrices, * gist-score-svm computes performance statistics from the outputs of gist-train-svm and gist-classify, * gist-rfe performs SVM recursive feature elimination on a given data set, * gist-sigmoid converts the discriminant values produced by gist-train-svm into probabilities, * gist2html converts an output file from one of the Gist programs into HTML format, and * gist-kernel computes a square kernel matrix from a given data file, using a user-specified list of kernel transformations. Gist is written in ANSI C. Source code, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

A Weblog on Bioinformatics, Genome Science and Next Generation Sequencing.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

This is the portal to the BLAST Server provided by the WUSTL Genome Ceneter BLAST Server. The Genome Center is a world leader in the fast-paced, constantly changing field of genomics. A truly unique institution, The Genome Center is pushing the limits of academic research by creating, testing, and implementing new approaches to the study of biology with the goal of understanding human health and disease, as well as evolution and the biology of other organisms. The Genome Center is helping to lead the way in high-speed, comprehensive genomics. Since its inception in 1993, The Genome Center has played a vital role in the field of genome sequencing, receiving over 800 million in funding. The Genome Center began as a key player in the Human Genome Project an international effort to decode all 3 billion letters of our genetic blueprint ultimately contributing 25 percent of the finished sequence. Sponsors: This resource is supported by the NIH. Keywords: Genome, BLAST, SErver, Genomics, Academic, Research,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains 4 probes per exon and no probes for exon-exon junctions, this new junction array averages 8 probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of a novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 exons validated out of 173 tested).

• Resource
• SciCrunch
• 16 years ago - by Anonymous

The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. Register for a free account.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

COPE is an encyclopedia of cytokines and has fully integrated subdictionaries on Angiogenesis, Apoptosis, Bacterial Modulins, CD Antigens, Cell lines, Eukaryotic cell types, Chemokines, CytokineTopics, Cytokine Concentrations in Body Fluids, Cytokine Inter-Species Reactivities, Dual identity proteins, Hematology, Innate Immunity Defense Proteins, Metalloproteinases, Protein domains, Regulatory peptide factors, Virokines, Viroceptors, and Virulence Factors. Most entries have a description as well as references.

• Resource
• SciCrunch
• 16 years ago - by Anonymous