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THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

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• SciCrunch
• 13 years ago - by Anonymous

Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.

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• SciCrunch
• 15 years ago - by Anonymous

A visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.

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• SciCrunch
• 13 years ago - by Anonymous

A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

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• SciCrunch
• 11 years ago - by Anonymous

Database of mutations associated with all major known forms of oculocutaneous and ocular albinism. The Albinism Database is part of the Locus Specific Mutation Databases of the Human Genome Variation Society and accepts the submission of new mutations. A link is provided for submission of new mutations. Columns in the database include: type of albinism, human locus, omim link, link to table of mutations and polymorphisms, and map of mutation locations.

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• SciCrunch
• 15 years ago - by Anonymous

A blog covering psychology, neuroscience, philosophy, quantum physics, and anything else worth writing about, by William Lu. William Lu is currently a postdoctoral fellow specializing in neuropsychology and rehabilitation psychology

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• 13 years ago - by Anonymous

A blog by a Romanian clinical psychologist and psychotherapist Lucia Grosaru. Major categories include: General, lifestyle, news, pensees, psychologists, psychotherapy, self-help and video. Lucia Grosaru is the President and a Founding Member of the Romanian Institute Sic Cogito, Founding Member for The Romanian Center of Psychology and a Founding Editor of The Romanian Journal of Psychology, Psychotherapy and Neuroscience. Lucia is an integrative psychotherapist, clinical psychologist and a Certified Rorschach Inkblot Test Specialist (Method: Scuola Romana Rorschach, Italy). She has graduated the Psychology and Educational Science Faculty at the University of Bucharest in 2008 and the Cognitive Psychodiagnosis and Counseling Master's Programme in 2010.

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• SciCrunch
• 13 years ago - by Anonymous

A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.

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• SciCrunch
• 15 years ago - by Anonymous

A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

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• SciCrunch
• 13 years ago - by Anonymous

Web services provided by the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC) to acquire data and metadata.

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• 11 years ago - by Anonymous

A web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. Analysis of a non-redundant test set, consisting of plant protein sequences provides a ~90% accuracy, whereas analysis of a similar set of nonplant protein sequences provides a ~92% accuracy. As input PredSL requires the protein's sequence in fasta format. The algorithm cosists of 11 steps: # Initially the 100 N-terminal residues of the sequence are coded (see supplementary material-neural network training) and fed to a first layer of 2 neural networks which determine whether a residue belongs or not to a chloroplast transit peptide (cTP) or a mitochondrial transit peptide (mTP). From this step we get 100 scores (one per residue) from each network. # We have set a cutoff where the residues do not belong to a transit peptide any longer, and thus we calculate two approximate cleavage sites from the 100 scores we calculated in step 1.(One from each network) # We take a window of 40 positions around the approximate cleavage site we estimated in step 2, and we use a set of neural networks to predict the cleavage site. Therefore we have one prediction of the cleavage site of the hypothetical cTP and one for the mTP. # We calculate the average of the scores of the hypothetical peptides predicted from each network, and this results to two scores. # We feed the 100 scores from step 1 to two neural networks (one for the cTP and one for the mTP), and we get two more scores. These scores represent the probability that the sequence has an mTP or a cTP. # We use PrediSi to calculate one more score for each sequence. This score represents the probability of a sequence belonging to a secreted protein. # We use a program that uses Markov chains to discriminate between two categories to get 6 more scores for the plant proteins and 3 more for the nonplant. (See supplementary material-Markov chains) # We use HMMER to get two additional scores for each protein. One that shows the existence or not of a cTP and one that shows the existence or not of an mTP. # We feed all the scores we gathered (13 for the plant and 7 for the non-plant proteins) to a neural network that does the final prediction. # Finally, if a sequence is predicted to belong to a chloroplast protein, we use HMMER to determine the existence of a lumenal-transit peptide (lTP) # If the user requires it, PredSL provides the possibility to make a graph for each case. The graphs for the chloroplast and mitochondrial sequences are created using the scores from Step 1 and taking a window around the predicted cleavage site from Step 3. For the secreted proteins, the graphs are created usind the hydrophobicity index (Kytte-Doolittle, 1982) for a window around the predicted cleavage site from PrediSi.

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• SciCrunch
• 14 years ago - by Anonymous

Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

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• SciCrunch
• 11 years ago - by Anonymous

Neuroamer is a researcher-oriented blog about neuroscience, psychiatry, and psychology. It is an attempt to fill the space between journal articles and pop science journalism.

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• SciCrunch
• 14 years ago - by Anonymous

The e-mouse.org is an online resource that aims to bring together and provide users with all information related to the laboratory mouse and its use as a model organism. Users can find direct links to MRB, a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, as well as the CreZOO, MMdb and Fleming Databases, three more specialized mouse repositories, all developed and hosted at the B.S.R.C. Alexander Fleming Institute. Additionally e-mouse.org provides links to major European and international mouse resources like the Mouse Genome Informatics (MGI), European Mouse Mutant Archive (EMMA), International Mouse Strain Resource (IMSR) and Ensembl. Users interested in retrieving information regarding the use of mouse models are encouraged to visit MRB which provides an index of publicly available mouse resources intended for both bench scientists and bioinformaticians. * Mouse Resource Browser (MRB) is a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, classified in 22 categories. * CreZOO is the European virtual repository of Cre and other targeted conditional driver strains. Its aim is to capture and disseminate extant and new information on all Cre driver strains. * MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. * Fleming Database is a fully searchable resource developed to host all mouse strains developed and/or housed in BSRC Al. Fleming's animal house. * MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. * EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. * IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. * Ensembl is a project that produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

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• SciCrunch
• 14 years ago - by Anonymous

Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.

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• SciCrunch
• 12 years ago - by Anonymous

The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.

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• SciCrunch
• 14 years ago - by Anonymous

ProQuest Dissertations and Theses Full text is a comprehensive collection of dissertations and theses, as well as the official digital dissertations archive for the Library of Congress and the database of record for graduate research. PQDT Full Text includes nearly 3 million searchable citations to dissertations and theses available for download in PDF format. The database offers full text for most of the dissertations added since 1997 and strong retrospective full-text coverage for older graduate works. Full-text dissertations are archived as submitted by the degree-granting institution. Each dissertation published since July 1980 includes a 350-word abstract written by the author. Masters theses published since 1988 include 150-word abstracts. Simple bibliographic citations are available for dissertations dating from 1637. ProQuest Dissertations and Theses Full Text also offers researchers unlimited access to digital copies from their own institutions as well as affordable copies from others.

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• SciCrunch
• 14 years ago - by Anonymous