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http://www.dhmc.org/goto/parkinson

A Parkinson's disease portal that provides information, materials, and programs to help Parkinson's patients and their care partners manage their everyday lives. The Center aims to enhance the quality of life for people with Parkinson's and their care partners and increase public awareness and education on Parkinson's disease. It provides resources for regional support group meetings, referrals to regional physicians, allied health professionals, home care agencies, and other resources, and information on current therapies and research programa. It also provides materials such as informational pamphlets and booklets, videos, DVDs, newsletters, and educational materials.

Proper citation: Parkinsons Center at Dartmouth-Hitchcock Medical Center (RRID:SCR_008096) Copy   

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http://www.cureparkinsons.org.uk

A patient led charity that funds research which will have an impact on the lives of people with Parkinson's, with the hope of an eventual cure for the condition. The Cure Parkinson's Trust has the clear goal of finding a cure for Parkinson's disease by investing in under resourced and underfunded projects that offer a possible cure in the future. This trust's primary role is identifying, funding and evaluating research projects, as well as hosting scientific forums to bring together relevant scientists within the field to discuss key areas of research and technology. Cure Parkinson's provides researchers with information on current research, research events, and the ability to apply for grants through the Cure Parkinson's Trust.

Proper citation: Cure Parkinson's Trust (RRID:SCR_008095) Copy   

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http://www.antibodies-online.com

Resells antibodies incorporating quality control metrics for antibody reagents. Antibodies-online is based in Germany and provides valuable content in terms of information about antibodies, recent research news and specific news about current antibodies. All these informations are generated by antibodies-online staff or external databases like Pubmed, EMBL Harvester or from Google Scholar.

Proper citation: Antibodies Online GmbH (RRID:SCR_008092) Copy   

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http://www.mouseatlas.org/

A portal to the Mouse Atlas of Gene Expression Project and Dissecting Gene Expression Networks in Mammalian Organogenesis Project. This Atlas will define the normal state for many tissues by determining, in a comprehensive and quantitative fashion, the number and identity of genes expressed throughout development. The resource will be comprehensive, quantitative, and publicly accessible, containing data on essentially all genes expressed throughout select stages of mouse development. Serial Analysis of Gene Expression (SAGE) is the gene expression methodology of choice for this work. Unlike expressed sequence tags (ESTs) and gene chip data, SAGE data are independent of prior gene discovery and are quantitative. Furthermore, SAGE data are digital, easily exchanged between laboratories for comparison and can be added to by scientists for years to come. Thus, this Atlas will include a data structure and data curation strategy that will facilitate the ongoing collection of gene expression data, even after the completion of this project. The Mouse Atlas project compromises 202 SAGE Libraries from 198 tissues. The list of libraries is available in a number of different groupings, including groups of libraries taken from specific tissue locations and libraries taken from specific developmental stages. Furthermore, this atlas will assemble gene expression profiles for a few focused experiments that will test hypotheses related to the techniques employed, tumor models and models of abnormal development. This will test the resource and provide quality control, validation and demonstrate applicability. Additionally, The Mammalian Organogenesis - Regulation by Gene Expression Networks (MORGEN) project will provide a complete, permanent, and accurate picture of mouse gene expression in the heart (atrioventricular canal and outflow tract), pancreas, and liver; new techniques to understand the interplay of proteins governing the expression of genes key to the development of these organ systems; and the identification of the master regulatory switches that control development of the tissues.

Proper citation: Mouse Gene Expression at the BC Cancer Agency (RRID:SCR_008091) Copy   

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http://bioinformatics.ekmd.huji.ac.il/milano/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MILANO provides a useful tool for the automatic custom annotation of microarray results which is based on all the available literature. It has two major advances over similar tools: the ability to expand gene names to include all their informative synonyms while removing synonyms that are not informative and access to the GeneRIF database which provides short summaries of curated articles relevant to known genes. MILANO allows annotation of lists of genes derived from microarray results by user defined terms. The annotation strategy is based on counting the number of literature co-occurrences of each gene on the list with a user defined term. This strategy allows the customization of the annotation procedure and thus overcomes one of the major limitations of the functional annotations usually provided with microarray results. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols that are likely to be less informative as literature searching terms. It supports searching two literature databases: GeneRIF and Medline (through PubMed), allowing retrieval of both quick and comprehensive results. MILANO''s ability can improve microarray analysis by analyzing a list of 150 genes that were affected by p53 overproduction. This analysis reveals that it enables immediate identification of known p53 target genes on this list and assists in sorting the list into genes known to be involved in p53 related pathways, apoptosis and cell cycle arrest. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment). The program is used by pasting the list of Gene ID''s or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms. Sample input is provided in the fields, so you can just click submit and see what happens. If you want to run data of your own, delete the sample input first.

Proper citation: Microarray Literature-based Annotation (RRID:SCR_008206) Copy   

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http://mitores.ba.itb.cnr.it

MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions. It integrates information from the most accredited world-wide databases to bring together gene, transcript and encoded protein sequences associated to annotations on species name and taxonomic classification, gene name, functional product, organelle localization, protein tissue specificity, Enzyme Classification (EC), Gene Ontology (GO) classification and links to other related public databases. The section Cluster, has been dedicated to the collection of data on protein clustering of the entire catalogue of MitoRes protein sequences based on all versus all global pair-wise alignments for assessing putative intra- and inter-species functional relationships. The current version of MitoRes is based on the UniProt release 4 and contains 64 different metazoan species. The incredible explosion of knowledge production in Biology in the past two decades has created a critical need for bioinformatic instruments able to manage data and facilitate their retrieval and analysis. Hundreds of biological databases have been produced and the integration of biological data from these different resources is very important when we want to focus our efforts towards the study of a particular layer of biological knowledge. MitoRes is a completely rebuilt edition of MitoNuc database, which has been extensively modified to deal successfully with the challenges of the post genomic era. Its goal is to represent a comprehensive and reliable resource supporting high-quality in-silico analyses aimed to the functional characterization of gene, transcript and amino acid sequences, encoded by the nuclear genome and involved in mitochondrial biogenesis, metabolism and pathological dysfunctions in metazoa. The central features of MitoRes are: # an integrated catalogue of protein, transcript and gene sequences and sub-sequences # a Web-based application composed of a wide spectrum of search/retrieval facilities # a sequence export manager allowing massive extraction of bio-sequences (genes, introns, exons, gene flanking regions, transcripts, UTRs, CDS, proteins and signal peptides) in FASTA, EMBL and GenBank formats. It is an interconnected knowledge management system based on a MySQL relational database, which ensures data consistency and integrity, and on a Web Graphical User Interface (GUI), built in Seagull PHP Framework, offering a wide range of search and sequence extraction facilities. The database is compiled extracting and integrating information from public resources and data generated by the MitoRes team. The MitoRes database consists of comprehensive sequence entries whose core data are protein, transcript and gene sequences and taxonomic information describing the biological source of the protein. Additional information include: bio-sequences structure and location, biological function of protein product and dynamic links to both, external public databases used as data resources and public databases reporting complementary information. The core entity of the MitoRes database is represented by the protein so that each MitoRes entry is generated for each protein reported in the UniProt database as a nuclear encoded protein involved in mitochondrial biogenesis and function. Sponsors: MitoRes has been supported by Ministero Universit e Ricerca Scientifica, Italy (PRIN, Programma Biotecnologie legge 95/95-MURST 5, Proiect MURST Cluster C03/2000, CEGBA). Currently it is supported by operating grants from the Ministero dellIstruzione, dellUniversit e della Ricerca (MIUR), Italy (PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929).

Proper citation: MitoRes (RRID:SCR_008208) Copy   

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http://medblast.sibsnet.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs.

Proper citation: MedBlast (RRID:SCR_008202) Copy   

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https://sites.google.com/site/dadadenoiser/

Infers both the sample genotypes and error parameters that produced a metagenome data set.

Proper citation: DADA (RRID:SCR_008205) Copy   

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http://compgen.bio.unipd.it/bioinfo/

Welcome to the computational genomics laboratory''s home page. Main research interests: computational biology, bioinformatics and systems biology applied to the study of the mechanisms underlying gene expression regulation. They also develop bioinformatic software aiming at helping the research community solve some problems.

Proper citation: Computational Genomics Laboratory (RRID:SCR_007901) Copy   

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http://www.ensembl.org/info/docs/tools/vep/index.html

Data analysis service to predict the functional consequences of known and unknown variants.

Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy   

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http://www.pragma-grid.net/

PRAGMA was formed to establish sustained collaborations and advance the use of grid technologies in applications among a community of investigators working with leading institutions around the Pacific Rim. Currently there are 35 institutions in PRAGMA, who meet twice a year at PRAGMA Workshops. In PRAGMA, applications are the key, integrating focus that bring together the necessary infrastructure and middleware to advance the applications goals. Sponsors: This resource is made possible by a grant from National Science Foundation Grant No. INT-0314015 and OCI-0627026.

Proper citation: Pacific Rim Applications and Grid Middleware Assembly (RRID:SCR_008225) Copy   

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http://pdbfun.uniroma2.it/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections.

Proper citation: Protein Databank Fun (RRID:SCR_008226) Copy   

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http://www.clunet.edu/BioDev/omm/gallery.htm

The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM''s exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand. Why devote a site to detailed visualizations of different macromolecules? In learning about the intricacies of life processes at the molecular level, it is important to understand how natural selection has fashioned the structure and chemistry of macromolecular machines to suit them for particular functions. This understanding is greatly facilitated by the visualization of 3-dimensional structure, when known. So, if static views of molecules (even in stereo) are worth a thousand words, then interactive animations of molecules should be worth much more. Indeed, we have found the types of displays represented here invaluable in gaining an appreciation for the details of key biochemical processes. Sponsors: This resource is federally-funded by the Protein Data Bank

Proper citation: Online Macromolecular Museum (RRID:SCR_008220) Copy   

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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   

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http://mmcd.nmrfam.wisc.edu/

A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

Proper citation: Madison Metabolomics Consortium Database (RRID:SCR_007803) Copy   

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http://www.upstate.edu/neuroscience/

The graduate program in Neuroscience is a multidisciplinary, interdepartmental program divided into three main areas: Cell and Molecular Neuroscience, Development and Regeneration, and Systems Neuroscience. Their research relates to many human diseases and disorders including fetal alcohol syndrome, spinal cord injury, degenerative retinal disease, Alzheimer''s disease, multiple sclerosis, cerebral palsy, and amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig''s disease.

Proper citation: SUNY Upstate Neuroscience (RRID:SCR_007913) Copy   

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http://mousemutant.jax.org/index.html

Producer and supplier of a collection of mice bearing spontaneous mutations. These mice contribute to a better understanding of the genetic bases of neurological, neuromuscular, sensory, metabolic, skeletal/craniofacial and developmental disorders and conditions such as diabetes, obesity and heart disease.

Proper citation: Mouse Mutant Resource (RRID:SCR_008367) Copy   

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http://www.scripps.edu/florida/

Research institute that focuses on basic biomedical science, drug discovery and technology development. The Scripps Florida research team focuses on the development of therapeutics in areas including neurology, cancer, the immune system, cardiovascular disease, metabolic disease, and infectious diseases. This institute has six departments: Cancer Biology, Molecular Therapeutics, Immunology and Microbial Science, Metabolism and Aging, Chemistry, and Molecular and Integrative Neurosciences. There is also the Translational Research Institute (TRI) which includes the following components: Discovery Biology, Drug Metabolism and Pharmacokinetics (DMPK), TRI-Informatics, Lead Identification and HTS, and Medicinal Chemistry. These groups collaborate in the discovery and development of new therapeutic agents. The Scripps Florida institute also offers a graduate program that emphasizes chemistry, chemical biology, biophysics and the biological sciences. This resource also provides a variety of programs for middle school, high school and college-age students to participate in research activities. These programs have a special emphasis on recruiting from historically underrepresented groups in the sciences.

Proper citation: Scripps Research Institute Florida Campus (RRID:SCR_008248) Copy   

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http://www.neuroptikon.org/

Neuroptikon is a tool for visualizing and interacting with neural circuits. Sponsors: This resource is supported by Janelia Farms.

Proper citation: Neuroptikon (RRID:SCR_008369) Copy   

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http://dbm.neuro.uni-jena.de/vbm/download/

This is the website of the Structural Brain Mapping Group at the Department of Psychiatry, University of Jena. Our principal research focuses on the development of methods for structural brain imaging and their application. Specific areas of interest include the investigation of structural brain plasticity and schizophrenia research. Regional structural brain changes are among the most robust biological findings in schizophrenia, yet the underlying pathophysiological changes remain poorly understood. Recent evidence suggests that abnormal neuronal/dendritic plasticity is related to alterations in membrane lipids. We examined whether serum activity of membrane lipid remodeling/repairing cytosolic phospholipase A2 (PLA2) were related to regional brain structure in magnetic resonance images (MRI). The study involved 24 schizophrenia patients, who were either drug-nave or off antipsychotic medication, and 25 healthy controls. Using voxel-based morphometry (VBM) analysis of T1-high-resolution MRI-images, we correlated both gray matter and white matter changes with serum PLA2-activity. PLA2 activity was increased in patients, consistent with previous findings. VBM group comparison of patients vs. controls showed abnormalities of frontal and medial temporal cortices/hippocampus, and left middle/superior temporal gyrus in first-episode patients. Group comparison of VBM/ PLA2-correlations revealed a distinct pattern of disease-related interactions between gray/white matter changes in patients and PLA2-activity: in first-episode patients (n = 13), PLA2-activity was associated with structural alterations in the left prefrontal cortex and the bilateral thalamus. Recurrent-episode patients (n = 11) showed a wide-spread pattern of associations between PLA2-activity and structural changes in the left (less right) prefrontal and inferior parietal cortex, the left (less right) thalamus and caudate nucleus, the left medial temporal and orbitofrontal cortex and anterior cingulum, and the cerebellum. Our findings demonstrate a potential association between membrane lipid biochemistry and focal brain structural abnormalities in schizophrenia. Differential patterns in first-episode vs. chronic patients might be related to PLA2-increase at disease-onset reflecting localized regenerative activity, whereas correlations in recurrent- episode patients might point to less specific neurodegenerative aspects of disease progression.

Proper citation: Structural Brain Mapping Group (RRID:SCR_008487) Copy   

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