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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   

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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   

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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   

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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.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   

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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   

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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   

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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   

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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   

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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   

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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   

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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   

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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   

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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   

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

Ontology that contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.

Proper citation: Cardiac Electrophysiology Ontology (RRID:SCR_007065) 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   

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http://brown.edu/academics/molecular-pharmacology-physiology-and-biotechnology/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20, 2021. Department of Molecular Pharmacology, Physiology, and Biotechnology has closed, effective June 30, 2021. Department of Molecular Pharmacology, Physiology and Biotechnology is basic science department within Brown Medical School, and is full participant in undergraduate based Program in Biology within Division of Biology and Medicine at Brown University.

Proper citation: Brown University Alpert Medical School Department of Molecular Pharmacology Physiology and Biotechnology (RRID:SCR_007222) Copy   

•   Source: SciCrunch Registry