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http://www.youngparkinsons.org/
An organization that is centered around the education of younger Parkinson's disease patients as well as their families, friends and healthcare professionals. They primarily provide educational and support programs and services that are designed to help younger Parkinson's patients manage the disease and maintain a healthy lifestyle. The center provides information about treatment options, clinical trials, support groups, person to person chats, local chapters,regional referral information, and Parkinson's related events.
Proper citation: American Parkinson's Disease Association National Young Onset Center (RRID:SCR_008102) Copy
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
Proper citation: MMSEQ (RRID:SCR_008184) Copy
The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.
Proper citation: CellML (RRID:SCR_008061) Copy
http://www.mf.uni-lj.si/bitola/
An interactive literature-based biomedical discovery support system. The goal of this system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database MEDLINE. To make the system more suitable for disease candidate-gene discovery and to decrease the number of candidate relations, we integrated background knowledge about the chromosomal location of the starting disease as well as the chromosomal location of the candidate genes from resources such as Entrez Gene, HUGO and OMIM. The BITOLA system can also be used as an alternative way of searching the Medline database. The system is available in two versions: closed discovery and open discovery. Closed discovery allows the input of two concepts (Example 1: a disorder and a gene. Example 2: a drug and a side effect) and generates potential explanations of the relationship between two entities. It does this by searching published literature to finds intermediate links. Open discovery allows the input of a single concept, then categories for first-order relatives of that concept, then categories for relatives of those first order concepts. Thus it can link from a disease to related drugs, then to genes related to those drugs and then test if those genes have been mentioned/tested in association with the disease. If the answer is no, then the gene is potentially related yet untested in the literature. Thus the open discovery tool is a nominator of new genes, drugs or neuroscience correlates to be investigated with diseases, disorders, physiological responses or any other phenotype.
Proper citation: BITOLA: Biomedical Discovery Support System (RRID:SCR_008175) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Movement Disorder Virtual University is the healthcare professional's source for movement disorder news, resources and educational activities. MDVU is brought to you by WE MOVE, a not-for-profit organization that has been educating and informing the movement disorder community for over a decade. WE MOVE believes that increased knowledge and understanding promote timely, accurate diagnosis and up-to-date treatment, resulting in a better quality of life for individuals affected by movement disorders. Educational Programs and Resources for Professionals WE MOVE's mission is to facilitate the communication of emerging clinical advances and therapeutic approaches to the management and treatment of movement disorders. Through its award-winning, HON-compliant Web site and as an accredited provider of continuing medical education (CME), WE MOVE strives to meet the educational needs of providers. WE MOVE develops up-to-date training programs and comprehensive, interactive teaching materials to assist professionals in deepening their understanding of neurologic movement disorders, their pathophysiology, etiology, differential diagnosis and state-of-the-art interventions. Case-based Learning (CBL) WE MOVE Case-based Learning (CBL) modules provide an environment that allows for participative learning a well-recognized tool to facilitate the adult learning experience. This self-paced, private learning environment encourages physicians to employ a problem-solving approach, walking step-by-step through the case history, family history, and symptomatology of the patient featured in the case. WE MOVE CBL modules illustrate the diagnostic process and varied approaches to treatment utilized by the thought leader who submitted the case, an invaluable experience for physicians looking to expand their expertise in the diagnosis and treatment of movement disorders. The depth of the WE MOVE CBL learning technology allows each case to highlight treatment of certain aspects of the condition or the efficacy of a given treatment regimen at different stages of disorder progression further enriching the physician's learning experience. For therapies requiring specific expertise in administration (e.g., injectable therapies), video footage of the therapeutic procedure itself enhances the depth of the experience. Co-location of WE MOVE CBL modules within the MDVU creates an unrivaled learning environment for physician education. WE MOVE CBL modules are available at no charge to physicians, 24 hours a day, seven days a week.
Proper citation: MDVU - Movement Disorder Virtual University (RRID:SCR_008050) Copy
http://www.shuttleworthfoundation.org/
Shuttleworth Foundation is supporting exceptional people to change the world. We provide funding for dynamic leaders who are at the forefront of social change. We identify amazing people, give them a fellowship grant, and multiply the money they put into their projects by a factor of ten or more. We are looking for social innovators who are helping to change the world for the better and are looking for some support through an innovative social investment model.
Proper citation: Shuttleworth Foundation (RRID:SCR_005930) Copy
http://www.nematodes.org/nematodegenomes/index.php/Main_Page
A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs.
Proper citation: 959 Nematode Genomes (RRID:SCR_006068) Copy
http://www.nematodes.org/NeglectedGenomes/MOLLUSCA/index.html
A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University.
Proper citation: MolluscDB PartiGene database (RRID:SCR_006069) Copy
MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided.
Proper citation: MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) Copy
mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.
Proper citation: mirEX (RRID:SCR_006060) Copy
The Foundation for Polish Science (FNP), formed in 1991, is an independent, self-financing, non-profit, non-governmental organization, with a mission of supporting science in Poland. It is the largest source of science funding in Poland outside the state budget. The main objectives of FNP are: * to support excellent scientists and research teams, * to facilitate technology transfer, * to support various investment initiatives serving science in Poland. The Foundation realizes these objectives by: * awarding individual prizes and scholarships to scientists, * awarding grants for the modernization of scientific facilities and the protection of scientific collections, * grants for the transfer of scientific achievements to industry, * otherwise supporting important undertakings in the service of science (e.g. through conferences and publishing programs). The Foundation also plays an increasingly active role in supporting international scientific cooperation, taking actions to facilitate the exchange of scientific ideas, and increasing the scientific independence of the younger generation of scientists.
Proper citation: Foundation for Polish Science (RRID:SCR_006062) Copy
http://afni.nimh.nih.gov/afni/
Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.
Proper citation: Analysis of Functional NeuroImages (RRID:SCR_005927) Copy
http://www.biocomputing.it/digit/index.php
The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements.
Proper citation: DIG IT - Database of Immunoglobulins and Integrated Tools (RRID:SCR_005924) Copy
http://cran.r-project.org/web/packages/aLFQ/
An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.
Proper citation: aLFQ (RRID:SCR_005925) Copy
http://ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R
Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.
Proper citation: IQRray (RRID:SCR_006057) Copy
NeuroGems is a collection of neuroinformatics software modules for data and modelling in neuroscience. The emphasis is on tools for collaboration, visualisation and use of open XML standards. The project was an escience pilot project funded by the UK MRC and BBSRC and based at the Universities of Edinburgh, Newcastle and UCL running from 2002 - 2005. Software Applications available: Textensor, Axiope, NeuroML, neuroConstruct, NClamp, RatBrain, 3D Atlas, Catacomb, Protsim1, Protsim2, Neosim1, Neosim2, Growth, Marching, Voxel, Patterns.
Proper citation: NeuroGEMS informatics software (RRID:SCR_006059) Copy
http://biodev.cea.fr/interevol/
InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface
Proper citation: InterEvol database (RRID:SCR_006054) Copy
http://ucsd.researchaccelerator.org/
Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity.
Proper citation: Research Accelerator (RRID:SCR_006051) Copy
A campus of the University of Massachusetts system, located in Pioneer Valley of Western Massachusetts.
Proper citation: University of Massachusetts Amherst; Massachusetts; USA (RRID:SCR_006052) Copy
SynDB is an online resource of proteins known or predicted to be related to the synapse or synaptic activity, and extensive information on the proteins'' functions, sequences, structures, expression, pathways, interactions, and disease associations. It is intended to be a repository of current knowledge and data as well as a starting point for future proteomics research in neurobiology. SynDB is the first focused database of the molecular biology of the synapse proteome. It contains the most comprehensive collection of proteins (13809 unique proteins spanning 1979 species and 104 protein domains, Aug 2006) that are known or predicted to be associated with synaptic activities. It integrates extensive information on protein functions, sequences, structures, expression, pathways, interactions, and disease associations. SynDB was generated using a combination of automated approaches, including keyword- and domain-based searches, and manual curation. It serves as a starting point for future neurobiology, neuropharmacology, and neuroinformatics research. Synapse ontology is a set of standard vocabulary which help to describe all synaptic gene products in a consistant way. As in common ontology, synapse ontolgy is composed of all the terms in a hierarchical structure, but specifically restricted to the function and structure annotation of synapse related gene products. Synapse ontology is a callaborative fruit of bioinformatists and neural biologists. Synapse ontolgy is aimed to describe all the synaptic molecules in terms of structure/biochemistry of synapse and physiology/function at synapse in a specied-independent manner. The controled vocabularies are hierarchically structured, so you can browser the related gene products in different levels: for example, you can find all the gene products of synaptic vesicle cycling or ion channels and receptors, or you can zoom in on all the gene products playing roles in the priming step of synaptic vesicle cycling.
Proper citation: SynDB: Synapse DataBase (RRID:SCR_005918) Copy
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