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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   

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http://www.crash2.lshtm.ac.uk

This is a trial for a large randomised placebo controlled trial among trauma patients with, or at risk of, significant haemorrhage, of the effects of antifibrinolytic treatment on death and transfusion requirement. Sponsors: This resource is supported by UK NIHR Health Technology Assessment programme, Pfizer, BUPA Foundation, and J P Moulton Charitable Foundation. Keyowrds: Trial, Placebo, Drug, Trauma, Haemorrhage, Antifibrinolytic, Treatment, Death, Transfusion,

Proper citation: Clinical Randomisation of an Antifibrinolytic in Significant Haemorrhage (RRID:SCR_007235) 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://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

http://ajp.psychiatryonline.org/audio.aspx

An audio summary of highlights and key articles from each issue of The American Journal of Psychiatry. Users may subscribe to the podcast to get automatic updates with each issue or download each issue''s audio file individually.

Proper citation: American Journal of Psychiatry Podcasts (RRID:SCR_007070) Copy   

•   Source: SciCrunch Registry

http://www.regardsstudy.org/

The REasons for Geographic and Racial Differences in Stroke (REGARDS) project, sponsored by the National Institutes of Health (NIH), is a national study focusing on learning more about the factors that increase a person''s risk of having a stroke. REGARDS is an observational study of risk factors for stroke in adults 45 years or older. 30,239 participants were recruited between January 2003 and October 2007. They completed a telephone interview followed by an in-home physical exam. Measurements included traditional risk factors such as blood pressure and cholesterol levels, and an echocardiogram of the heart. At six month intervals, participants are contacted by phone to ask about stroke symptoms, hospitalizations and general health status. The study is ongoing and will follow participants for many years. The purpose of the REGARDS project is to understand why people in some parts of the country develop more strokes than people in other parts of the country, and why blacks develop more strokes than whites. We hope to learn how to reduce the number of people having strokes.

Proper citation: REGARDS - REasons for Geographic and Racial Differences in Stroke (RRID:SCR_007228) Copy   

•   Source: SciCrunch Registry

http://medgen.ugent.be/rtprimerdb/

Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry.

Proper citation: RTPrimerDB- The Real-Time PCR and Probe Database (RRID:SCR_007106) Copy   

•   Source: SciCrunch Registry

http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/cd-hit/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CD-HIT (RRID:SCR_007105) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/combine_rts2000.shtm

Software program that performs the auto-alignment and the composition of images to create the mosaic.

Proper citation: Combine RTS2000 (RRID:SCR_007104) Copy   

•   Source: SciCrunch Registry

http://ani.embl.de/4DXpress

This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data.

Proper citation: Expression Database in 4D (RRID:SCR_007066) Copy   

•   Source: SciCrunch Registry

http://www.bmdw.org

Bone Marrow Donors Worldwide (BMDW) is the continuing effort to collect the HLA phenotypes of volunteer stem cell donors and cord blood units, and is responsible for the co-ordination of their worldwide distribution. Participants are 63 stem cell donor registries from 44 countries, and 43 cord blood banks from 25 countries. The current number of donors and cord blood units in the BMDW database is: 14,605,618 (14,178,976 donors and 426,642 CBU''s The original goal to collect the HLA phenotypes of volunteer stem cell donors and cord blood units, and to co-ordinate their world-wide distribution remain their primary goals. But new initiatives have been added: - To maximise the chance of finding a stem cell donor or cord blood unit by providing access to all stem cell donors and cord blood units available in the world. - To minimise the effort required for stem cell donor or cord blood unit searches: only registries with potential stem cell donors or cord blood units need to be contacted. - To provide an estimate of the chance of finding a stem cell donor or cord blood unit for a given patient. - To provide advanced search programs to identify partially matched stem cell donors or cord blood units. - To facilitate search advice requests via the Internet. - To facilitate improvements in family search strategies. - To provide relevant general information for the benefit of the patient. - To provide statistics on the increase of different registries, the number of DNA typed donors, etc. Sponsors: Bone Marrow Donors Worldwide is an initiative of the Immunobiology Working Party of the European Group of Blood and Marrow Transplantation (EBMT) in 1988. Keyworss: Bone marrow, Donor, Cell, Phenotype, Stem cell, Cord blood unit,

Proper citation: Bone Marrow Donors Worldwide (RRID:SCR_007186) Copy   

•   Source: SciCrunch Registry

http://bayesiananalysis.wustl.edu

Welcome to the Bayesian Analysis of Common NMR Problems software home page. This Bayesian analysis software is a series of programs with a Java interface that use Bayesian probability theory to solve common data analysis problems that occur in the sciences and in NMR in particular. Click here for a complete list of the applications addressed. The programs that run the various Bayesian analysis, the server software, were developed at Washington University by Dr. G. Larry Bretthorst and the Java language client interface was developed by Dr. Karen Marutyan. The combination of the server and client software is called the Bayesian Analysis of Common NMR Problems software. However, this name is slightly misleading because this software can analyze data from many different sources, not just NMR data. Additionally, unlike the previous interface to this software, this new interface does not require the user to have access to any specialized NMR software, i.e., this interface is completely independent of Varian''s VnmrJ, although the interface can load and process data from a Varian spectrometer. Sponsors: This resource is supported by the Washington University in St. Louis. Keywords: Analysis, Software, Java, Theory, Science, NMR, Server, Data, Spectrometer,

Proper citation: Bayesian Analysis of Common NMR Problems (RRID:SCR_007182) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/

Public university in Reading, Berkshire, England. It was founded in 1892 as University College, Reading, a University of Oxford extension college.

Proper citation: University of Reading; Reading; United Kingdom (RRID:SCR_007135) Copy   

•   Source: SciCrunch Registry

http://biodata.mshri.on.ca/osprey/servlet/Index

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical representations from Geno Ontology (GO) annotated interaction data maintained by The Grid. The following list describes some of the important characteristics of the Osprey Network Visualization System: * Portability ( cross platform availability ) o Osprey is available on almost all Platforms that support the latest Java Plugin * Tools for Biological Analysis o Osprey provides many features such as network filters, connectivity filters, advanced layouts, and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data * Powerful Support Database o Integrated with Osprey is a powerful database of interactions and annotation, see section 8. The GRID ( The General Repository of Interaction Datasets ). * Ease of use o Osprey provides an extremely user friendly interface for working with interaction data * Online Database Add-on Ability o Osprey can be incorporated as a standard visualization tool with online databases such as The GRID * Support for figures o Osprey networks can be saved in SVG, PNG and JPG format so they can be used with image programs Sponsors: Development of Osprey was funded by a grant from the Canadian Institutes of Health Research.

Proper citation: Osprey: Network Visualization System (RRID:SCR_007138) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/software_downloads/biorat/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. An information extraction (IE) tool specifically designed to perform biomedical IE and which is able to locate and analyze both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE.

Proper citation: BioRAT (RRID:SCR_007099) Copy   

•   Source: SciCrunch Registry

http://earthref.org/MAGIC/

Databases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database.

Proper citation: Magnetics Information Consortium (RRID:SCR_007098) Copy   

•   Source: SciCrunch Registry