Tools   Select Another Resource Report Type

https://www.hpcwire.com/2005/10/28/swami_the_next_generation_biology_workbench/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release.

Proper citation: Swami: The Next Generation Biology Workbench (RRID:SCR_007217) Copy   

•   Source: SciCrunch Registry

http://titan.biotec.uiuc.edu/ESTIMA/

A web application called Expressed Sequence Tag Information Management and Annotation (ESTIMA) has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against arbitrary reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/download/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee.

Proper citation: ESTIMA - Expressed Sequence Tag Information Management and Annotation (RRID:SCR_007216) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/neuro/

Neuroscience research at BU is coordinated through unified community of investigators from multiple research groups of Charles River and MED campuses.Neuroscience faculty support Undergraduate Program in Neuroscience and Graduate Program for Neuroscience. Students can get specialized training in additional disciplines while carrying out neuroscience thesis research (Anatomy & Neurobiology, Biology, and Pharmacology and Experimental Therapeutics).

Proper citation: Boston University Department of Neuroscience (RRID:SCR_007218) Copy   

•   Source: SciCrunch Registry

http://biorobotics.org

This is portal takes you to the BioRobotics Laboratory website. Keywords: Laboratory, Software, Robot, Robotics, Biology,

Proper citation: BioRobotics Laboratory (RRID:SCR_007176) Copy   

•   Source: SciCrunch Registry

http://www.americanheart.org/

The American Heart Association (AHA) publishes medical scientific statements on various cardiovascular disease and stroke topics. AHA volunteer scientists and healthcare professionals write the papers. The statements are supported by scientific studies published in recognized journals and have a rigorous review and approval process. Scientific statements generally include a review of data available on a specific subject, an evaluation on its relationship to overall cardiovascular disease science, and often an American Heart Association position on the basis of that evaluation. The American Heart Association sponsors accredited scientific conferences and professional development seminars to disseminate new and emerging scientific knowledge and stimulate discussion on future research and the application of knowledge. Keywords: Heart, Cardiovascular, Disease, Stroke, Volunteer, Scientist, Healthcare, Development, Knowledge,

Proper citation: American Heart Association (RRID:SCR_007210) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/WSsas/

SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions.

Proper citation: WSsas - Web Service for the SAS tool (RRID:SCR_007051) Copy   

•   Source: SciCrunch Registry

http://neurocommons.org/

The Neurocommons project is an Open Source knowledge management platform for biological research. It seeks to make all scientific research materials - research articles, annotations, data, physical materials - as available and as usable as they can be. We do this by both fostering practices that render information in a form that promotes uniform access by computational agents - sometimes called interoperability. We want knowledge sources to combine meaningfully, enabling semantically precise queries that span multiple information sources. Our work covers general data and knowledge sources used in computational biology as well as sources specific to neuroscience and neuromedicine. The practices that we develop and promote are designed to play well on the Semantic Web. We view our technical work not as creating a new service or content library, although we do both, but rather as helping to promote the growth of semantically linked scientific information.

Proper citation: The NeuroCommons Project (RRID:SCR_007171) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CCON

Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.

Proper citation: Cerrado concepts and plant community dynamics (RRID:SCR_007174) Copy   

•   Source: SciCrunch Registry

http://chao.stat.nthu.edu.tw/

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....

Proper citation: Professor Anne Chaos Website (RRID:SCR_007205) Copy   

•   Source: SciCrunch Registry

http://www.cs.unm.edu/~moret/GRAPPA/

As fascinating as diversity is, it''s not the sort of thing that computational scientists usually get excited about. Uncovering how diversity came to be has captured the attention of a team of researchers at Alliance partner University of New Mexico and the University of Texas, though. Using the 512-processor LosLobos Linux Pentium III supercomputing cluster at the Albuquerque High Performance Computing Center, the team has created a phylogeny reconstruction - or evolutionary history - of 12 bluebell species, predicting all of the steps that take these species back to a single common ancestor. To meet the challenge, they created a whole new piece of software known as GRAPPA. GRAPPA is is free software available as a gzipped tar file containing all source files needed to compile an executable version.

Proper citation: GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms (RRID:SCR_007208) Copy   

•   Source: SciCrunch Registry

http://www.poweratlas.org/

The Power Atlas is a web-based resource to assist investigators in the planning and design of microarray and expression based experiments. This software is currently aimed at estimating the power and sample size for a two group comparison based upon pilot data. The methods underlying the web site are reported in Gadbury et al (2004) and the software is described in further detail at Page et al (2006). There are two ways to use the Power Atlas: 1. We have downloaded the datasets currently in the Gene Expression Omnibus (GEO) and processed each of them with our power analysis software. Investigators may search among the datasets for the experiment that most closely resembles their proposed project and get sample size and power estimates. 2. Investigators may upload their own preliminary data and the program will extrapolate power from this dataset.

Proper citation: Power Atlas (RRID:SCR_007207) Copy   

•   Source: SciCrunch Registry

https://hpc.nih.gov/systems/

The NIH Biowulf cluster is a GNU/Linux parallel processing system designed and built at the National Institutes of Health and managed by the Helix Systems Staff. The system is designed for large numbers of simultaneous jobs common in bioinformatics as well as large-scale distributed memory tasks such as molecular dynamics. Sponsor: This work was supported by the National Institutes of Health Intramural Research Program through the Center for Information Technology and the National Institute of Neurological Disorders and Stroke, and by the Internal National Institute of Standards and Technology Research Fund. Keywords: Software, Program, Processing, System, Simulatenous, Bioinformatics, Memory, Molecular, Dynamics,

Proper citation: Biowulf at the NIH (RRID:SCR_007169) Copy   

•   Source: SciCrunch Registry

http://www.azcert.org

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).

Proper citation: Arizona Center for Education and Research on Therapeutics (RRID:SCR_007201) Copy   

•   Source: SciCrunch Registry

http://www.port.ac.uk/research/exrc/

Supports researchers using Xenopus models. Researchers are encouraged to deposit Xenopus transgenic and mutant lines, Xenopus in situ hybridization probes, Xenopus specific antibodies and Xenopus expression clones with the Centre. EXRC staff perform quality assurance testing on these reagents and then make them available to researchers at cost. Supplies wild-type Xenopus, embryos, oocytes and Xenopus tropicalis fosmids.

Proper citation: European Xenopus Resource Center (RRID:SCR_007164) Copy   

•   Source: SciCrunch Registry

http://www.bio.brandeis.edu/undergrad/neuro/index.html

Students entering Neuroscience Program at Brandeis have opportunities to work in range of fields, from cognitive neuroscience to structure and function of ion channels. Undergraduate concentration in neuroscience is designed to provide interdisciplinary program of study of neural mechanisms involved in control of human or animal behavior. Program is especially appropriate for students wishing to pursue further study in medicine, experimental psychology, or neuroscience.

Proper citation: Brandeis University Neuroscience Undergraduate Program (RRID:SCR_007166) Copy   

•   Source: SciCrunch Registry

http://www.ecolicommunity.org/

Sixty years of study have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its great importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub uses web services that are being developed to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life. :topical portal;

Proper citation: EcoliHub (RRID:SCR_007114) Copy   

•   Source: SciCrunch Registry

http://www.neuroconstruct.org/

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.

Proper citation: neuroConstruct (RRID:SCR_007197) Copy   

•   Source: SciCrunch Registry

http://www.genoscope.cns.fr/externe/tetraodon/

The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.

Proper citation: Tetraodon Genome Browser (RRID:SCR_007079) Copy   

•   Source: SciCrunch Registry

http://pharmacology.uthscsa.edu/

The Department of Pharmacology at the Health Science Center at San Antonio is uniquely positioned to carry out research into the most relevant areas in pharmacology as well as to deliver superior training in pharmacology. Our faculty use approaches that range from the molecular and cellular through electrophysiology and systems to behavior. The Department of Pharmacology at the University of Texas Health Science Center at San Antonio (UTHSCSA) has 18 tenure-track or tenured faculty, 11 research-track faculty, 15 graduate students, and 15 postdoctoral fellows. We are very excited about recent developments in pharmacology that allow new and challenging means of exploring the biological effects of drugs. Graduate studies leading to a Doctor of Philosophy degree in the basic biomedical sciences at UTHSCSA are offered in the Integrated Multidisciplinary Graduate Program (IMGP). The Department of Pharmacology administers two tracks within the IMGP: the pharmacology track and the neuroscience track. The Department of Pharmacology has a ten-week summer research program that offers participants a variety of experiences that will help prepare them for success in research-intensive doctoral programs. Participants will have research responsibilities, attend seminars, actively participate in a student journal club and take part in formal course work. Prior research experience is not necessary, and students of all undergraduate levels are encouraged to apply.

Proper citation: University of Texas Health Science Center at San Antonio Department of Pharmacology (RRID:SCR_007078) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/

Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health.

Proper citation: Broad Institute (RRID:SCR_007073) Copy   

•   Source: SciCrunch Registry