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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) Copy   

•   Source: SciCrunch Registry

https://biosharing.org/collection/MIBBI

A common portal for minimum information (MI) checklists to act as a one-stop shop for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration. Goals include * To increase the visibility of projects developing guidance for the reporting of biological and biomedical science. * To encourage appropriate collaborative development between projects to avoid duplication of effort or competition. * To promote the adoption of consensus guidance on reporting by journals and funders.

Proper citation: Minimum Information for Biological and Biomedical Investigations (RRID:SCR_002042) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/biomodels-main/

Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.

Proper citation: BioModels (RRID:SCR_001993) Copy   

•   Source: SciCrunch Registry

https://www.nei.nih.gov/learn-about-eye-health/outreach-resources/national-eye-health-education-program

NEI established NEHEP to increase awareness among healthcare professionals and the public of scientifically based health information that can be applied to preserving sight and preventing blindness. NEHEP works in partnership with a variety of public and private organizations that conduct eye health education programs. Program activities are designed to promote the importance of early detection and timely treatment of eye disease and the use of vision rehabilitation services using strategies that are culturally appropriate, health-literate, and evidence-based. NEHEP ensures that vision is a health priority by translating eye and vision research into public and professional education programs. NEHEP supports collaboration among eye health professionals, healthcare providers, patients, and the public. NEHEP programs provide healthcare professionals with information, materials, and resources to educate patients and the public about eye health and the importance of comprehensive dilated eye examinations. NEHEP is supported by a Planning Committee and a Partnership, which bring a vast array of knowledge about eye health and experience with populations at higher risk for eye disease. NEHEP Programs *Diabetic Eye Disease: The NEHEP Diabetic Eye Disease (DED) Education Program is designed to increase awareness about DED among people with diabetes, particularly those at higher risk. *Glaucoma: The NEHEP Glaucoma Education Program provides information about glaucoma to people at higher risk as well as those living with the disease. *Low Vision: The NEHEP Low Vision Education Program is designed to create awareness among adults, their families and friends, and the general public about vision rehabilitation services. *Ojo con su Vision: Ojo con su visin or Watch out for your vision is the Spanish-language program of NEHEP that targets the Hispanic/Latino community. Healthy Vision Program Healthy People 2010, the health promotion and disease prevention framework for the Nation, identifies the most significant risks to health and establishes national goals to reduce those risks. Focus area 28 of Healthy People 2010, Vision and Hearing, includes 10 vision objectives known as Healthy Vision. The Healthy Vision objectives identify national eye health concerns, and encourage individuals, organizations, and businesses to help address these concerns in their communities. *Healthy Vision 2010 Focusing on examination and prevention, eye diseases, injury and safety, and vision rehabilitation, Healthy Vision 2010 is designed to help you determine what you can do in your home, community, business, or state to help improve the Nation's eye health. *Healthy Vision Community Awards Program The Healthy Vision Community Awards Program provides awards of up to 10,000 for community-based eye health education programs. The program objectives address examinations and prevention, eye diseases, injury and safety, and vision rehabilitation. *Healthy Vision Month May is Healthy Vision Month, a national eye health observance sponsored by NEI and the National Eye Health Education Program Partnership. Healthy Vision Month is devoted to elevating vision as a public health priority. Each year focuses on a specific eye health topic. *Healthy Vision Community Programs Database The Healthy Vision Community Programs Database is a searchable collection of community-based vision health programs from the different U.S. states and territories. It stimulates ideas for creative eye health education projects and promotes networking among interested groups. Outlook Newsletter: Outlook is the electronic newsletter of the National Eye Health Education Program (NEHEP). Outlook provides quarterly updates on eye health education, disease prevention activities, and NEHEP activities and materials. Related Research: NEHEP represents an extension of the support that NEI provides to vision research, where results are disseminated to health professionals, patients, and the public.

Proper citation: National Eye Health Education Program (RRID:SCR_002049) Copy   

•   Source: SciCrunch Registry

http://www.cs.sunysb.edu/~skiena/shorty/

Software for targeted de novo assembly of microreads with mate pair information and sequencing errors.

Proper citation: SHORTY (RRID:SCR_002048) Copy   

•   Source: SciCrunch Registry

http://www.aspgd.org/

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

Proper citation: ASPGD (RRID:SCR_002047) Copy   

•   Source: SciCrunch Registry

http://bbrfoundation.org/

The Brain and Behavior Research Foundation (formerly NARSAD, the National Alliance for Research on Schizophrenia and Depression) is committed to alleviating the suffering of mental illness by awarding grants that will lead to advances and breakthroughs in scientific research. Additionally, learn about brain and behavior disorders and upcoming events.
100% of all donor contributions for research are invested in NARSAD Grants leading to discoveries in understanding causes and improving treatments of disorders in children and adults, such as depression, bipolar disorder, schizophrenia, autism, attention deficit hyperactivity disorder, and anxiety disorders like obsessive-compulsive and post-traumatic stress disorders. Over a quarter of a century, we have awarded nearly $300 million worldwide to more than 3,000 scientists carefully selected by our prestigious Scientific Council. We receive no government funding. All of our work relies on contributions from families, foundations and other caring donors.

Proper citation: Brain and Behavior Research Foundation (RRID:SCR_001992) Copy   

•   Source: SciCrunch Registry

http://brainmapping.org/

This is a topical portal dedicated to the communication of news, science, and information of interest to the brain mapping community, and to sharing and promoting the science of brain mapping. The purpose and goal of brain mapping is to advance the understanding of the relationship between structure and function in the human brain. Scientists in this field seek to gain knowledge of the physical processes that underly human sensation, attention, awareness and cognition. These results are immediately applicable to surgical intervention, to the design of medical interventions and to the treatment of psychological and psychiatric disorders.

Proper citation: www.brainmapping.org (RRID:SCR_001987) Copy   

•   Source: SciCrunch Registry

http://www.worldpdcongress.org

A nonprofit organization dedicated to providing an international forum for the latest scientific discoveries, medical practices and caregiver initiatives related to Parkinson's disease. It hosts the annual World Parkinson Congress, an event which focuses on bringing physicians, scientists, allied health professionals, caregivers and people diagnosed with Parkinson's disease together, in order to create a global dialogue that will help expedite treatment practices and the discovery of a cure .

Proper citation: World Parkinson Congress (RRID:SCR_002034) Copy   

•   Source: SciCrunch Registry

http://mpss.danforthcenter.org/

Informational portal that aggregates information about databases for next gen sequencing.

Proper citation: NextGen Sequence Databases (RRID:SCR_002152) Copy   

•   Source: SciCrunch Registry

http://www.wpda.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The World Parkinson's Disease Association is an alliance of members from all over the world who have come together to share information about Parkinson's disease. In order to further Parkinson's research and better the condition of those diagnosed with the disease, the Association: establishes computerized connections; takes part in and/or finances research activities; urges pharmaceutical companies and government institutions of the various countries to support the guidelines recommended by the associations of Parkinson's patients; and coordinates and promotes interchange of information among its members with the aim of solving problems of mutual interest.

Proper citation: World Parkinson Disease Association (RRID:SCR_002035) Copy   

•   Source: SciCrunch Registry