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THIS RESOURCE IS NO LONGER IN SERVICE; documented April 28, 2016. A blog which seeks to inform users on different neurological conditions. These conditions include Alzheimer's, brain tumors, epilepsy, Parkinson's disease, sleep disorders, psychiatric conditions, stroke, and spine conditions.

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• SciCrunch
• 15 years ago - by Anonymous

Java toolset for working with next generation sequencing data in the BAM format.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

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• SciCrunch
• 13 years ago - by Anonymous

The Transverse Myelitis Association was established in 1994 as an organization dedicated to advocacy for those who have these rare neuroimmunologic diseases. It was incorporated as a not-for-profit organization in 1996. It facilitates support and networking opportunities amongst families; provides educational information; functions as a clearinghouse for articles and research literature; and investigates, advocates for and supports research and innovative treatment efforts. Transverse Myelitis is a rare neurological disorder that is part of a spectrum of neuroimmunologic diseases of the central nervous system. Other disorders in this spectrum include, Acute Disseminated Encephalomyelitis (ADEM), Optic Neuritis, and Neuromyelitis Optica (Devic''s disease). The membership of The Transverse Myelitis Association includes persons with all of these disorders, their family members and caregivers and the medical professionals who treat people with these disorders. The TMA publishes a newsletter for our members twice a year, which contains articles by physicians and health care providers. There are also articles written by people with the rare neuroimmunologic disorders. A membership directory is published and distributed annually. The TMA assists in the development of local support groups and is involved in various fund-raising efforts, such as Reading for Rachel, to raise awareness and funds for research. The TMA supports and conducts various symposiums and workshops involving both professionals and patients for the exchange of information regarding research and treatment strategies for persons with the rare neuroimmunologic disorders of the central nervous system.

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• SciCrunch
• 16 years ago - by Anonymous

A database of miRNA-mRNA interactions. The interaction data is obtained from various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction.

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• SciCrunch
• 13 years ago - by Anonymous

Matlab routines for analyzing psychophysical data * sychometric function fitting * Multi-condition model fitting * Adaptive procedures * Signal detection measures * Maximum likelihood difference scaling * Model comparisons

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• SciCrunch
• 13 years ago - by Anonymous

Database of images, movies, and protocols to promote a comprehensive understanding of plant organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles. It consists of 5 individual parts, ''Perceptive Organelles Database'', ''The Organelles Movie Database'', ''The Organellome Database'', ''The Functional Analysis Database'', and ''External Links to other databases and Web pages''. All the data and protocols in ''The Organelle Movie Database'', ''The Organellome Database'' and ''The Functional Analysis Database'' are populated by direct submission of experimentally determined data from plant researchers. Your active contributions by submission of data and protocols to our database would also be appreciated. * Perceptive Organelles Database: This database contains images and movies of organelles in various tissues during different developmental stages in response to environmental stimuli. * Organelles Movie Database: This database contains time-lapse images, Z slices and projection images of organelles in various tissues during different developmental stages, visualized using fluorescent and non-fluorescent probes. * Organellome Database: This database contains images for cellular structures that are composed of organelle images in various tissues during different developmental stages, visualized with fluorescent and non-fluorescent probes. * Functional Analysis Database: This database is a collection of protocols for plant organelle research. * External Links: Access to biological databases.

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• SciCrunch
• 14 years ago - by Anonymous

The LSU Epilepsy Center of Excellence is dedicated to providing state-of-the-art, comprehensive epilepsy treatment, enhancing access to epilepsy education for patients and physicians, and promoting multidisciplinary epilepsy research in pharmacology, neuroelectrophysiology, neuroimaging, neurosurgery, neuropsychology, biomedical engineering and public health. The center''s team of professionals offers diagnostic and presurgical monitoring, the strategic use of antiepileptic medications, specialized epilepsy neuroimaging, vagus nerve stimulator implantation, ketogenic diet management, neuropsychological testing, psychiatric support and epilepsy surgery for adults and children. The Center also hosts several clinical research trials each year for investigational medications and devices. The following are the treatment methods currently available at this center: - Epilepsy Brain Implants - Responsive Neurostimulator (RNS) - Medications - Medication blood level monitoring - Vagus Nerve Stimulators (VNS) - Epilepsy Surgery - Ketogenic Diet - Psychiatric Services - Radiosurgery Epilepsy Center Sections: *Electrophysiology *Neuroimaging *Neuropsychology *Neuroscience *Neurosurgery *Pharmacology *Psychiatry *Research

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• SciCrunch
• 17 years ago - by Anonymous

A fungal rDNA internal transcribed spacer (ITS) sequence database (although additional genes and genetic markers are also welcome) to facilitate identification of environmental samples of fungal DNA. Additional important features include user annotation of INSD sequences to add metadata on, e.g., locality, habitat, soil, climate, and interacting taxa. The user can furthermore annotate INSD sequences with additional species identifications that will appear in the results of any analyses done. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. In addition, it also holds all fungal ITS sequences in the International Nucleotide Sequence Databases (INSD: NCBI, EMBL, DDBJ). Both sets of sequences may be used in any analyses carried out. UNITE is accompanied by a project management system called PlutoF, where users can store field data, document the sequencing lab procedures, manage sequences, and make analyses. PlutoF intends to make it possible for taxonomists, ecologists, and biogeographers to use a common platform for data storage, handling, and analyses, with the intent of facilitating an integration of these disciplines. A user can have an unlimited number of projects but still make analyses across any project data available to him.

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• SciCrunch
• 16 years ago - by Anonymous

Database supports use of mouse model system for human cancer by providing comprehensive resource for data and information on various tumor models.

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• SciCrunch
• 17 years ago - by Anonymous

Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing.

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• SciCrunch
• 13 years ago - by Anonymous

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

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• SciCrunch
• 14 years ago - by Anonymous

Blog about molecules, minds and everything in between, written by Mo, a molecular and developmental neurobiologist turned science writer. He aims to produce well-written and easily accessible articles about all aspects of neuroscience, so that he might help to improve public understanding of it. This blog has been featured for two consecutive years in the Open Lab annual anthologies of the best science blogging. AFTER four years at ScienceBlogs.com, Neurophilosophy has moved to a new home. It is now hosted by The Guardian.

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• SciCrunch
• 16 years ago - by Anonymous

A software package for the discovery of regulatory regions from Bis-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Database of authoritative health information about diseases, conditions, and wellness issues that offers reliable, up-to-date health information for free. It contains the latest treatments, information on drugs and supplements, the meanings of words, and medical videos and illustrations. Links to the latest topic or disease specific medical research or clinical trials are also offered. * MedlinePlus pages contain carefully selected links to Web resources with health information on over 900 topics. ** The MedlinePlus health topic pages include links to current news on the topic and related information. You can also find preformulated searches of the MEDLINE/PubMed database, which allow you to find references to latest health professional articles on your topic. * The A.D.A.M. medical encyclopedia brings health consumers an extensive library of medical images and videos, as well as over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. * The Merriam-Webster medical dictionary allows you to look up definitions and spellings of medical words. * Drug and supplement information is available from the American Society of Health-System Pharmacists (ASHP) via AHFS Consumer Medication Information, and Natural Medicines Comprehensive Database Consumer Version. ** AHFS Consumer Medication Information provides extensive information about more than 1,000 brand name and generic prescription and over-the-counter drugs, including side effects, precautions and storage for each drug. ** Natural Medicines Comprehensive Database Consumer Version is an evidence-based collection of information on alternative treatments. MedlinePlus has 100 monographs on herbs and supplements. * Interactive tutorials from the Patient Education Institute explain over 165 procedures and conditions in easy-to-read language. An XML File for the MedlinePlus Health Topics is available, http://www.nlm.nih.gov/medlineplus/xmldescription.html. The ontology is available through Bioportal, http://bioportal.bioontology.org/ontologies/MEDLINEPLUS

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• SciCrunch
• 17 years ago - by Anonymous

Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.

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• SciCrunch
• 16 years ago - by Anonymous

Nine centers that conduct clinical trials and basic research on new immune-based therapies for autoimmune diseases. This program enhances interactions between scientists and clinicians in order to accelerate the translation of research findings into medical applications. By promoting better coordination and communication, and enabling limited resources to be pooled, ACEs is one of NIAID''''s primary vehicles for both expanding our knowledge and improving our ability to effectively prevent and treat autoimmune diseases. This coordinated approach incorporates key recommendations of the NIH Autoimmune Diseases Research Plan and will ensure progress in identifying new and highly effective therapies for autoimmune diseases. ACEs is advancing the search for effective treatments through: * Diverse Autoimmunity Expertise Medical researchers at ACEs include rheumatologists, neurologists, gastroenterologists, and endocrinologists who are among the elite in their respective fields. * Strong Mechanistic Foundation ACEs augment each clinical trial with extensive basic studies designed to enhance understanding of the mechanisms responsible for tolerance initiation, maintenance, or loss, including the role of cytokines, regulatory T cells, and accessory cells, to name a few. * Streamlined Patient Recruitment The cooperative nature of ACEs helps scientists recruit patients from distinct geographical areas. The rigorous clinical and basic science approach of ACEs helps maintain a high level of treatment and analysis, enabling informative comparisons between patient groups.

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• dkNET
• 14 years ago - by Anonymous

Xiamen University, colloquially known as Xia Da in Mandarin Chinese or Ha Tai in Xiamen dialect, is public research university in Xiamen, Fujian, China with strengths in economics and management, fine arts, law, chemistry, journalism, communication, and mathematics.

• Organization
• SciCrunch
• 17 years ago - submitted by Eddy Kim

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

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• SciCrunch
• 15 years ago - by Anonymous

A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous