Curator Dashboard

A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

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• SciCrunch
• 13 years ago - by Anonymous

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

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• SciCrunch
• 17 years ago - by Anonymous

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

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• SciCrunch
• 13 years ago - by Anonymous

Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.

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• SciCrunch
• 15 years ago - by Anonymous

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

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• SciCrunch
• 17 years ago - by Anonymous

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

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• SciCrunch
• 13 years ago - by Anonymous

A R package for multiple marker meta-analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Next-generation genome browser software designed for the latest generation of genome data.

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• SciCrunch
• 13 years ago - by Anonymous

A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.

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• SciCrunch
• 17 years ago - by Anonymous

Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

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• SciCrunch
• 17 years ago - by Anonymous

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

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• SciCrunch
• 17 years ago - by Anonymous

The mission of the Morehouse School of Medicine Neuroscience Institute (MSMNI) is to create a supportive and challenging environment for the investigation and teaching of the functional organization of the nervous system, and to seek ways to reduce suffering brought about by neurological disorders. Members of the MSM NI are involved in teaching graduate students, medical students, and health care professionals about researching and treating medical conditions that are caused by or are rooted in the central nervous system. Additionally, MSM NI offers an 8-week Summer Research Program to qualified undergraduate, post-baccalaureate and first-year medical school students. Funding and administrative support were secured from the National Institutes of Health Office on Research for Minority Health and the National Institute for Neurological Disorders and Stroke (NINDS), respectively. The Neuroscience Institute is composed of selected faculty members from the Department of Neurobiology and the Department of Pharmacology at Morehouse School of Medicine who are conducting grant supported research. MSMNI research areas cover a broad range of cellular and molecular neuroscience and include the molecular biology and physiology of circadian rhythm, mechanisms of sleep and sleep disorders, mechanisms of stroke and stroke prevention, photoreceptor and retinal physiology, glutamate receptor physiology and mechanisms of hyperexcitability in epilepsy. Investigators use a variety of experimental preparations including whole animals, the intact portions of the central nervous system, and simplified preparations, such as tissue slices and single cells, to study cellular activities and cell-cell communication under more controlled conditions.

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• SciCrunch
• 17 years ago - by Anonymous

At the Department of Pharmacology & Toxicology at Michigan State University, we combine integrative research, active learning and intellectual enrichment to prepare the student for advancement and leadership in their chosen field. The Department provides courses for undergraduate students, graduate students, medical students of the allopathic, osteopathic and veterinary colleges, and nursing students. In addition, specialized courses of study are offered in areas of professional development and life-long learning. From molecular and cellular levels to organ systems and whole animal models, our graduate and undergraduate programs encompass multiple areas of study, empowering students to challenge the boundaries of knowledge and chart their own unique path in the biomedical sciences. The disciplines of pharmacology and toxicology play a momentous role in human health today, and their applications in the professional world are vast. The department offers: * Pharmacology & Toxicology Graduate Doctoral Program * Online MS Programs ** Online Professional Science Masters in Integrative Pharmacology ** Online Masters in Pharmacology * Undergraduate Courses in Pharmacology & Toxicology * Dual Major Graduate Program in Toxicology (joint Pharmacology & Toxicology/Environmental Toxicology graduate program) * NIGMS Integrative and Organ Systems Pharmacology Short Course * Summer Undergraduate Research Fellowships

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.

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• SciCrunch
• 13 years ago - by Anonymous

A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

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• SciCrunch
• 12 years ago - by Anonymous

Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences.

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• SciCrunch
• 17 years ago - by Anonymous

The mission of the Department of Pharmaceutical Sciences is to make scholarly contributions to the discipline of pharmaceutical sciences and related fields. Education within the department offers a high quality learning environment that includes Ph.D. and Pharm.D./Ph.D. degree programs. Although not required for entry into pharmacy practice, a one-year residency is offered and affords the Pharm.D. graduate an opportunity to develop expertise in clinical pharmacy practice and specialty areas. The graduate program leading to the Ph.D. degree in pharmaceutical sciences is designed for students seeking teaching and research careers in academic institutions, the pharmaceutical industry and other health-related agencies. An interdisciplinary approach prepares graduates to perform independent research, to encourage scholarly development and to acquire teaching skills. Areas of specialization include pharmacology, pharmaceutics, toxicology, and medicinal chemistry. The Doctor of Pharmacy (Pharm.D.)/Doctor of Philosophy (Ph.D.) Degree Program enables highly qualified students to obtain both degrees in a shortened period of time. This Pharm.D./Ph.D. Degree program is designed primarily for students who are strongly motivated toward an academic/ research career in the pharmaceutical sciences. The Program is flexible enough to accommodate individuals of varied educational backgrounds.

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• SciCrunch
• 16 years ago - by Anonymous

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

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• SciCrunch
• 13 years ago - by Anonymous

Graduate Program in Pharmacology at Meharry Medical College embraces the broad definition of pharmacology as the study of how chemical agents affect living processes; the chemicals involved include agents such as endogenous hormones, neurotransmitters, and/or growth factors; toxic substances in our environment; and pharmaceutically developed drugs. The breadth of our scientific environment is manifested by faculty who study the fate of drugs once ingested and the variability of drug response in varying patient populations (a discipline known as pharmacokinetics), as well as faculty who study the mechanisms by which drugs and endogenous agents work (a discipline known as pharmacodynamics). A unique strength of our research and training environment is the inter-disciplinary nature of the program, which encompasses faculty from the four divisions of the Department of Biomedical Science and Departments of Internal Medicine and Neurology.

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• SciCrunch
• 17 years ago - by Anonymous

Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

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• SciCrunch
• 12 years ago - by Anonymous