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http://www.blki.hu/~szucs/OS3.html

Orbital Spike is a tool for time series analysis. It contains a wide range of methods to analyze data from point processes such as spike arrival times, heart beats or other behavioral episodes. It is optimized this program for spike trains but it works with other types of data, too. The program can analyze up to 8 channels recorded simultaneously each containing a maximum of 132,000 events (spikes). Assuming an average firing rate of 10 Hz for a neuron, you can then analyze a time series of approximately 3 and half hours long. There are up to 8 panels shown in the Orbital Spike desktop. The panels will contain the kind of data of interest. The graphs are associated with a bunch of parameters like window width, bin size, resolution, delay etc. All these parameters are listed in the parameter box, which appears on the right side of the desktop. It is pretty easy to change the parameters and what is nice, the corresponding graph(s) will be recalculated immediately. You can also use a dialog box to change parameters. There are a lot of functions, statistics, graphs and diagrams available. A few of them are: * Interspike interval sequences * ISI Poincar * maps or return maps Instantaneous firing rate * ISI histograms and probability densities * Joint ISI and MSI probability densitograms * Autocorrelation, crosscorrelation * Spike density functions using kernel estimators * Fourier-amplitude spectrum and spectogram * Symbolic maps, recurrence plots * Phase plots of spike density functions Sponsors: Support for this work came from the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Engineering and Geosciences, under Grants DE-FG03-90ER14138 and DE-FG03-96ER14592; from the Office of Naval Research under Grant N00014-00-1-0181; from the National Science Foundation under Grant PHY0097134; from the National Institutes of Health under Grants R01 NS-40110-01A2 and 1RO1 NS-40110; and from the Army Research Office under Contract DAAD19-01-1-0026. R. D. Pinto was supported by the State of Sao Paulo Research Foundation (FAPESP).

Proper citation: Spike Train Analysis Software by Attila Szucs: Orbital Spike 4 (RRID:SCR_001868) Copy   

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http://pga.gs.washington.edu

The SeattleSNPs PGA is focused on identifying, genotyping, and modeling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans. SeattleSNPs is focused on variation analysis in genes related to the inflammatory response. These gene targets are found in specific pathways and from interacting molecules contributing to this response. Available Resources: - Baseline assembled and complete genomic sequence and chromosomal location for candidate gene targets - Mapping of exon and repeat structure for candidate genes - Amplification primers and conditions - SNPs mapped by location in gene structure - SNPs with immediate surrounding sequence for genotype assay design - Genotypes and relative allele frequencies of the SNPs - Special features of SNPs - location (5', coding, etc.), amino acid substitutions, recurrent variation - Manuals on all protocols, data analysis procedures, and use of software tools - Workshop on genetic variation analysis and a gene submission program for variation analysis Sponsors: SeattleSNPs is funded as part of the National Heart Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).

Proper citation: SeattleSNPs - Variation Discovery Resource (RRID:SCR_001859) Copy   

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https://www.hgsc.bcm.edu/content/sea-urchin-genome-project

Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.

Proper citation: Sea Urchin Genome Project (RRID:SCR_001735) Copy   

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http://www.nesys.uio.no/Atlas3D/

A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

Proper citation: Atlas3D (RRID:SCR_001808) Copy   

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http://www.intute.ac.uk/

Intute is a free online service that helps you to find the best web resources for your studies and research. It was created in response to users' needs and the changing Internet information environment. With millions of resources available on the Internet, it can be difficult to find useful material. The Intute subject specialists review and evaluate thousands of resources to help you choose the key websites in your subject. Intute can also help you develop your Internet research skills through our Virtual Training Suite tutorials, written by lecturers and librarians from universities across the UK. The discipline focus of their service is delivered through four new subject groups: * Science, Engineering and Technology (including geography) * Arts and Humanities * Social Sciences * Health and Life Sciences Intute is created by a consortium of seven universities, working together with a whole host of partners. The Intute consortium includes: * University of Birmingham * University of Bristol * Heriot-Watt University * The University of Manchester * Manchester Metropolitan University * University of Nottingham * University of Oxford Sponsors: Intute is funded by the Joint Information Systems Committee (JISC).

Proper citation: Intute: The Best Web Resources For Education and Research (RRID:SCR_001764) Copy   

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http://protein.bio.unipd.it/pasta2/

Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.

Proper citation: Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) Copy   

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http://www.bioit.org.cn/ao/aobase

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. AOBase is a database for antisense oligonucleotides (AOs) selection and design. AOBase is a database developed to facilitate Antisense Oligonucleotides (ODNs) selection for gene expression modulation and to provide a free data source for computer aided ODNs design. Information about valid and invalid ODNs reported in literature are collected and stored in the database, including oligo sequences, target sequences, secondary structures of the target sites, oligo activity measured, and the assay type used for activity measurement. The details on target RNA molecules and reference literature can be explored through the hyperlinks linked to GenBank and PubMed respectively. Each record can be searched for via two web retrieval interfaces: 1) TargetSearch interface, which allows users to query ODNs by name, accession number, or only imprecise descriptions of its target RNA; 2) AOSearch interface, which allows users to search ODNs with several parameters combined, such as oligo activity measured, oligo concentration applied, and motifs involved in oligo sequences. With these two retrieval interfaces, AOBase can be used to select effective ODNs for gene function exploration without expensive in vitro screening experiments, and contribute to mining rules for rational ODNs design. A user friendly interface to encourage data submission is provided.

Proper citation: Database for Antisense Oligonucleotides Selection and Design (RRID:SCR_001753) Copy   

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http://www.nitrc.org/projects/plink

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

Proper citation: PLINK (RRID:SCR_001757) Copy   

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http://www.oege.org/

Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity.

Proper citation: Online Encyclopedia for Genetic Epidemiology studies (RRID:SCR_001825) Copy   

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http://meme-suite.org/

Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy   

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https://www.bioconductor.org/packages//2.10/bioc/html/spade.html

An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.

Proper citation: SPADE (RRID:SCR_001810) Copy   

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http://sammeth.net/confluence/display/ASTA/2+-+Download

Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc.

Proper citation: AStalavista (RRID:SCR_001815) Copy   

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http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

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https://www.snpstats.net/

A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate)

Proper citation: SNPSTATS (RRID:SCR_002142) Copy   

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http://www.PDtrials.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A collaborative initiative of Parkinson's organizations dedicated to increasing education and awareness about clinical research. PDtrials provides up-to-date information on Parkinson's disease trials currently enrolling participants in the U.S. and Canada, as well as information about Parkinson's studies for people living with PD, their families and caregivers. Researchers can list their own trials on the PDtrials website. Patients can browse trial listings by type, location, symptom, or keyword.

Proper citation: PDtrials- Parkinsons Disease Clinical Trials (RRID:SCR_002027) Copy   

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http://compbio.dfci.harvard.edu/tgi/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description. In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated. DATABASES *Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group. *GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID. *Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10 *Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools: *TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets. *GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems. *clview: an assembly file viewer. *SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. *cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases. *DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com.

Proper citation: Gene Index Project (RRID:SCR_002148) Copy   

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http://sharcgs.molgen.mpg.de/

Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.

Proper citation: SHARCGS (RRID:SCR_002026) Copy   

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http://cinteny.cchmc.org/

Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

Proper citation: Cinteny (RRID:SCR_002147) Copy   

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http://neuron.duke.edu/cells/download.html

Online platform for visualizing and editing the morphology of neurons. Written in Java.

Proper citation: Cvapp (RRID:SCR_002095) Copy   

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http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx

Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.

Proper citation: SNP Function Portal (RRID:SCR_001954) Copy   

•   Source: SciCrunch Registry