Curator Dashboard

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

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• SciCrunch
• 12 years ago - by Anonymous

The UCSD School of Medicine are dedicated to producing future leaders in all areas of medicine. As such, the School promotes the pursuit of dual degrees, either in the Medical School's own graduate degree programs or programs offered in other disciplines in the institution. In addition to the study of medicine, the School of Medicine actively encourages its student body to explore broadly in various scholarly areas related to the biomedical sciences. The goal of this additional training is to produce graduates who will bring fresh, innovative ideas to the research laboratory, the public health sector, the humanities and the social sciences, and the business environment. Students may elect to obtain advanced degrees in the following areas: * Biomedical Sciences * Masters in Bioengineering * Masters in Public Health * Masters in Leadership of Health Care Organizations * Masters of Advanced Studies in Clinical Research * Ph.D. Program in the Humanities and Social Sciences * Independent Ph.D. programs Opportunities for enrollment in research or degree programs outside of UCSD are also available, and students are encouraged to investigate these, if interested. Sponsors: This program is supported by the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

The Graduate Program in Neurosciences at the University of California, San Diego offers an outstanding opportunity for graduate training in one of the most highly interactive scientific environments available in the United States. Recently, our graduate program was named by the National Research Council of the National Academy of Sciences as the top-ranking neuroscience graduate program in the country. The faculty who participate in the Graduate Program in Neurosciences have been brought together from many campus departments, the School of Medicine and from a number of affiliated institutes, including the Salk Institute, the Scripps Research Institute, the Scripps Institute of Oceanography, the UCSD Medical Center, and the Veterans Administration Medical Center. Because there is an enormous breadth of neuroscience research interests represented among the faculty, students are able to pursue study in a wide range of neuroscience areas and they often carry out their dissertation research in collaboration with more than one laboratory. Sponsors: FUnding for this program comes from the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. <BR/> Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.<BR/>

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• SciCrunch
• 17 years ago - by Anonymous

Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithm. This software is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. See the GNU General Public License for more details. For a copy of the GNU General Public License, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. Sponsors: Jinx presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050. open source license, GNU general public license

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• SciCrunch
• 17 years ago - by Anonymous

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

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• SciCrunch
• 14 years ago - by Anonymous

Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. 02111-1307, USA. Sponsors: ImageJ Mosaic Plug-Ins software presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050.

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• SciCrunch
• 17 years ago - by Anonymous

Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.

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• SciCrunch
• 17 years ago - by Anonymous

Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.

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• SciCrunch
• 14 years ago - by Anonymous

Commercial antibody supplier that specializes in the development and manufacture of viral antigens and anti-viral antibodies for diagnosis, monitoring, and treatment of significant viral infectious diseases.

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• SciCrunch
• 14 years ago - by Anonymous

The Department of Psychiatry at the University of California, San Diego is one of the most innovative and productive academic departments of psychiatry in the country. The guiding principle in this development has been that the educational and research programs of a psychiatry department must be at the cutting edge and encompass and integrate the most current innovations in the field with those approaches from the past which have proven to be valid and effective. The department has a strong commitment to the dynamic understanding of an individual's current social context and feelings, and past behaviors and experiences. We believe we have created one of the best available integrations of the biopsychosocial approaches to understanding normal and abnormal human behavior. By design, a rich diversity of scientific and clinical strategies are represented within the department, but the core organizing ethic of our educational and training programs is a profound commitment to our patients well being. It is the department's conviction that clinical psychiatry can only be learned in the context of meaningful interaction and contact with patients. The Residency Training Program is developmental in nature, appropriately challenging the residents at each level as they move from intensively supervised beginners to autonomous, confident, skilled clinicians and colleagues at graduation. The training occurs within the department's ambiance of collegiality, enthusiasm, openness of communication, intellectual and scientific rigor, and spirit of inquiry, which characterize our highly productive and energetic faculty. The UCSD faculty represent a virtual who's who of world-class basic and clinical scientists and clinicians, all of whom are available and participate in our residents training and experiences. The tradition at UCSD, both on the general campus and within the School of Medicine, is that of academic excellence. The department shares in this tradition and expects it from its faculty, trainees, and students. The goal of the residency program is to develop highly competent psychiatric physicians and leaders who are comprehensively trained in the most up-to-date diagnostic and treatment techniques which have proven effective for the full spectrum of mental disorders.

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• SciCrunch
• 15 years ago - by Anonymous

The Computational Neuroscience specialization is a new facet of the broader Neuroscience graduate program at UCSD. The goal of the specialization is to train the next generation of neuroscientists with the broad range of computational and analytical skills that are essential to understand the organization and function of complex neural systems. The specialization is intended for students with backgrounds in neuroscience, physics, chemistry, biology, psychology, computer science, engineering, and mathematics. This specialization allows Neuroscience students to concentrate on a focused program of rigorous course work in both the theoretical and experimental aspects of computational neuroscience. Students are encouraged to pursue thesis research that includes both an experimental and a computational component, often arranged by the student as a collaboration between two research groups. The program is focused on these major themes relevant for computational neuroscience research: - Neurobiology of Neural Systems - the anatomy, physiology, and behavior of systems of neurons, with emphasis on basic phenomenology. - Advanced Measurement Tools in Neuroscience - Advanced imaging and recording techniques reflecting the impact of experimental physics on neuroscience. - Algorithms for the Analysis of Neural Data - New algorithms and techniques for analyzing data obtained from physiological recording - Theoretical Basis for Collective Neural Dynamics - A synthesis of approaches from mathematics and physical sciences as well as biology will be used to explore the collective properties and nonlinear dynamics of neuronal systems. Sponsors: This program is supported by the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

The Center for Medicinal Cannabis Research (CMCR) will conduct high quality scientific studies intended to ascertain the general medical safety and efficacy of cannabis products and examine alternative forms of cannabis administration. The Center will be seen as a model resource for health policy planning by virtue of its close collaboration with federal, state, and academic entities. The objectives of this center are: 1. To conduct and support focused controlled clinical trials on the efficacy of cannabis in patients diagnosed with HIV/AIDS, cancer, seizures or muscle spasms associated with a chronic debilitating condition, or any other serious condition providing sufficient theoretical justification. 2. To use prospective clinical trials to determine optimal dosage, timing, and modes of administration for cannabis in various medical disorders. 3. To conduct randomized trials to compare the efficacy and safety of various methods of cannabis administration. 4. To conduct observational studies and randomized trials to assess the safety and toxicity of cannabis in the medically ill. Such studies will evaluate the impact of treatment on daily functioning and on life quality. 5. To conduct limited pre-clinical studies with direct relevance to understanding cannabis as a therapeutic agent. 6. To facilitate the implementation of research by assisting investigators in securing relevant regulatory review and approval by state and federal agencies. 7. To establish a process of rigorous peer review of scientific proposals. 8. To secure external sources of funding to maximize the scope and size of cannabis studies. Sponsors: This resource is supported by the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

The UCSD ADRC conducts a wide variety of research studies dedicated to understanding the causes, clinical features, and treatments for Alzheimer's disease and related memory disorders. The goal of the center is to discover ways to prevent and eradicate the disease. The Center aims to maintain research subjects, clinical resources, and clinical data to support ongoing and proposed research and to assist in the development of new clinical and interdisciplinary research. An Alzheimer's brain bank with well characterized cases, including Mild Cognitive Impairment and Lewy Body disease, is maintained at the Center.

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• SciCrunch
• 16 years ago - by Anonymous

We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterize SNPs between specific groups of individuals or within genes with predicted function. The system is flexible and researchers may add additional levels of annotation, and perform novel queries specific to their area of interest. If you have sequence data you'd like to include please contact Dave Edwards.

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• SciCrunch
• 17 years ago - by Anonymous

This UCSD department, the first Cognitive Science Department in the world, provides a focus for the continued evolution of the discipline of cognitive science. Cognitive science is a diverse field unifying three broad categories: the brain, behavior and computation. It's the study of how people, animals and computers think, act and learn. In order to understand the mind/brain, cognitive science brings together the methods and discoveries from neuroscience, psychology, linguistics, anthropology, philosophy and computer science. The interdisciplinary aspects of cognitive science continue to flourish, and the participation of the broader cognitive science community on campus continues to be fundamental to cognitive science as practiced at UCSD. The interdisciplinary Ph.D. program continues to be offered as a degree option (in addition to the departmental Ph.D.), with participation by members of the Departments of Anthropology, Biology, Cognitive Science, Communication, Computer Science and Engineering, Linguistics, Music, Neuroscience, Philosophy, Psychiatry, Psychology, and Sociology. Cognitive Science is a relatively young field that focuses on conducting new research into the field or applying existing knowledge into new applications. This Department contains several research labs each specializing in different areas and the Department's faculty has also been published many times in various publications. Sponsors: This department is supported by the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

Neuroscience is a multidisciplinary approach to understanding nervous systems at levels ranging from the molecular and cellular to the whole organism. The goal of this Program is to prepare students for careers in research, teaching and/or scientific administration. Students are expected to learn the fundamentals of neuroscience, starting with a required core sequence, become knowledgeable concerning a range of research methods as taught in a required neuroscience laboratory course, and demonstrate capability in original research. Graduate student training ultimately reflects the research competence and specialties of the faculty, that is, the specific research training received by a graduate student is the responsibility of the major professor/mentor under whose guidance and in whose laboratory the student carries out the research projects leading to the degree. Students will benefit from an interdisciplinary training approach, tailored by the major advisor but enriched by the readily available expertise and laboratory facilities of program faculty with backgrounds ranging from chemistry to psychology. In addition to this training, it is our intention, through outside speakers and planned forums, to make students aware of alternate careers open to neuroscientists whose interests and talents might lead to areas such as biotechnology, science administration and the like. The Interdepartmental Ph.D Program in Neuroscience at UC Riverside is aimed at providing high quality graduate training for students who come from a variety of undergraduate backgrounds but share a commitment and an intense interest in nervous system research. We currently have nineteen faculty with expertise in various aspects of neuroscience and whose principal appointments are in the Departments of Biology, Cell Biology &amp; Neuroscience, Chemistry, Entomology, and Psychology, and the Division of Biomedical Sciences. A major part of training in neuroscience is in supervised laboratory research, the student working with one or more of the neuroscience faculty.

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• SciCrunch
• 14 years ago - by Anonymous

The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities.

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• SciCrunch
• 17 years ago - by Anonymous