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Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

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• SciCrunch
• 15 years ago - by Anonymous

A database providing access to mRNA sequences and associated regulatory elements. Users can obtain data relating to translation (by species in a non-redundant format), search for regulatory elements in a defined set, or search their own sequence for known regulatory elements. The mRNA sequences are processed from Genbank, including complete genomes. They are divided into biologically relevant sections 5' UTRs and 3' UTRs, initiation and termination regions and the full CDS sequences. This data or your own sequences can be searched for defined regulatory elements. Recent Developments The web interface has been revised to allow users to analyse their own sequences. All motifs description have been revised new specific patterns have been added. Transterm data was updated with Genbank 122 (Feb 2001). Acknowledgements Health Research Council of New Zealand Marsden Fund of New Zealand translation, translational control of protein synthesis, mRNA, biologically relevant mRNA regions, GenBank, taxonomy, initiation codon (Kozaks consensus or Shine Dalgarno sequences), termination codon, coding regions or 3' flanking regions, Nucleotide Sequence, Transcriptional regulator, transcription factor

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• SciCrunch
• 17 years ago - by Anonymous

The Hungarian Academy of Sciences is the most important and prestigious learned society of Hungary. Its seat is at the bank of the Danube in Budapest, between Széchenyi rakpart and Akadémia utca.

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

A text mining derived database with focus on extracting and classifying gene-disease associations with respect to several biomolecular conditions. It uses a machine learning based algorithm to extract semantic gene-disease relations from a textual source of interest. The semantic gene-disease relations were extracted with F-measures of 78. More specifically, the textual source utilized here originates from Entrez Gene''''s GeneRIF (Gene Reference Into Function) database (Mitchell, et al., 2003). LHGDN was created based on a GeneRIF version from March 31st, 2009, consisting of 414241 phrases. These phrases were further restricted to the organism Homo sapiens, which resulted in a total of 178004 phrases. We benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function) phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph. We extend the framework of Conditional Random Fields towards the annotation of semantic relations from text and apply it to the biomedical domain. Our approach is based on a rich set of textual features and achieves a performance that is competitive to leading approaches. The model is quite general and can be extended to handle arbitrary biological entities and relation types. The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining.

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• SciCrunch
• 14 years ago - by Anonymous

By collecting and analyzing blood samples from Geisinger''s large patient population, MyCode will help unlock the mysteries of some of the most devastating and debilitating diseases. Blood samples are obtained from patients of certain Geisinger specialty clinics to study specific conditions, such as obesity and cardiovascular disease, and also from patients of Geisinger primary care clinics to provide a representative sample of the regional population. More than 60,000 samples from over 23,000 Geisinger patients have been collected so far, and sample collection is ongoing. MyCode researchers use the blood samples to study the genetic causes of diseases and certain disease-related molecular mediators. Knowledge gained from these studies will allow researchers to pursue innovative approaches to disease prevention, diagnosis and treatment. To be of value for Genomic Medicine research, bio-banked samples must be connected to clinical data: MyCode allows genetic and molecular data about the samples to be connected to medical data in a way that protects patient identity. When a patient agrees to participate in MyCode, blood samples for the MyCode Project are collected during blood draws ordered as part of the patient''s routine medical care. After the sample is drawn and labeled, a staff member from the Weis Center for Research transports the blood to the Geisinger Clinic Genomics Core (GCGC) where it is processed for storage. At this stage, all personal identification markers are removed and the samples are assigned a randomly-selected identification number. A secure key is maintained that allows approved researchers to connect the samples to the clinical data for genomic studies in a way that ensures confidentiality of the information. To maintain confidentiality of MyCode data the code linking the research numbers and the electronic health records are kept in a password-protected files accessible only to MyCode team members. Additionally, all results generated from the samples are reported as a group so that individuals are not identified. The samples are stored indefinitely.

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• SciCrunch
• 16 years ago - by Anonymous

Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand.

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• SciCrunch
• 13 years ago - by Anonymous

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

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• SciCrunch
• 13 years ago - by Anonymous

A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally.

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• SciCrunch
• 13 years ago - by Anonymous

Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design.

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• SciCrunch
• 13 years ago - by Anonymous

Established in 1986, the Center for AIDS Prevention Studies (CAPS) at the University California, San Francisco (UCSF) is the world''s largest research center dedicated to social, behavioral, and policy science approaches to HIV. The mission of the CAPS is to conduct research to prevent new HIV infections, improve health outcomes among those infected, and reduce disparities. This is how we do it: * CAPS provides core support for multidisciplinary and high-impact HIV research, enhances the excellence of research projects, trains a new generation of HIV scientists, and assists implementing partners. * Our Administrative Core provides strong leadership and management to stimulate innovative research and ensure scientific rigor and sound fiscal operations. * Our Developmental Core fosters innovative, high-impact, multidisciplinary HIV research by providing funds for innovative pilot work, sponsoring training and education, and ensuring the scientific excellence of research. * Our Methods Core provides comprehensive methodological training and consultation in research design, qualitative and quantitative analysis, and state-of-the-art data collection and management. * Our Policy and Ethics Core stimulates and supports policy-relevant research, identifies and analyzes the policy and ethics implications of research, and ensures the highest ethical conduct of research. * Our Technology and Information Exchange (Domestic Response) Core responds to the domestic epidemic by disseminating information, fostering community collaborative research, providing technical assistance and capacity-building to community-based organizations, and learning from community expertise. * Our Global Response Core responds to the global epidemic by fostering collaborative research with scientists in developing countries, completing and disseminating Cochrane Collaborative scientific reviews, and providing technical assistance, capacity building, and an evidence base to implementing partners.

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• SciCrunch
• 15 years ago - by Anonymous

A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

The SYNERGY Clinical Research Unit (CRU) is an outpatient research support unit that offers investigators a full array of services for the conduct of clinical research. The CRU is available to any Dartmouth faculty or researcher wishing to access dedicated space and staff resources for the efficient conduct of clinical research.

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• SciCrunch
• 13 years ago - by Anonymous

Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia.

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• SciCrunch
• 15 years ago - by Anonymous

TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. For each organism, its complete membrane transport complement was identified, classified into protein families according to the TC classification system, and functional predictions are provided.For each organism, a summary page is available, overviewing the whole transporter system, including transporter types and individual transporter families. For individual transporter types, a detailed list of transporters with their possible substrates is shown with links to individual protein page which contains protein sequence and annotation information. You can also compare the transporter system from two or more different organisms. A search engine is set up for easy search in our transporter database for transporter type, family, individual proteins and their substrates. You can also blast search your protein sequence against our transporter database.With the rapid development of genomic sequencing both in TIGR and in other institutes, more and more genomes are available for the analysis of their transporter system. We will keep updating this site with the newly published genomes. If you have any suggestions, corrections, or comments on our site, please contact us. We are currently working on providing additional functionality for this database.

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• SciCrunch
• 17 years ago - by Anonymous

NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities.

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• SciCrunch
• 15 years ago - by Anonymous

Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site.

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• SciCrunch
• 13 years ago - by Anonymous

Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes.

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• SciCrunch
• 17 years ago - by Anonymous

University founded in 1938, is a higher education institution in Changsha, Hunan Province. The university is a national 211 Project university, one of 100 key universities in the 21st century that enjoy priority in obtaining national funds.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web.

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• SciCrunch
• 15 years ago - by Anonymous

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

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• SciCrunch
• 13 years ago - by Anonymous