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The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center.

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• SciCrunch
• 17 years ago - by Anonymous

Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience.

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• SciCrunch
• 17 years ago - by Anonymous

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An M software package for Clustering 16S rRNA sequences into operational taxonomic units (OTUs). The download link contain the package and some benchmark data sets.

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• SciCrunch
• 13 years ago - by Anonymous

An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.

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• SciCrunch
• 12 years ago - by Anonymous

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

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• SciCrunch
• 13 years ago - by Anonymous

A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.

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• SciCrunch
• 12 years ago - by Anonymous

The Journal of Cerebral Blood Flow & Metabolism stands at the interface between basic and clinical neurovascular research, and features timely and relevant research highlighting experimental, theoretical, and clinical aspects of brain circulation, metabolism and imaging. The journal is relevant to any physician or scientist with an interest in brain function, cerebrovascular disease, cerebral vascular regulation and brain metabolism, including neurologists, neurochemists, physiologists, pharmacologists, anesthesiologists, neuroradiologists, neurosurgeons, neuropathologists and neuroscientists. On this website, you will find the full text of articles published online weekly, in advance of print, the current issue and an archive of previous issues. You can also find general information about the journal, and more detailed information for readers, authors, referees, librarians, advertisers, and journalists. Most articles are published online before they appear in print. New papers are uploaded weekly to the Advance online publication (AOP) page. The online publication date is specified for each paper; these versions are identical to the printed version in every respect and may be cited using the digital object identifier (DOI).

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• SciCrunch
• 16 years ago - by Anonymous

Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.

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• SciCrunch
• 12 years ago - by Anonymous

Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/

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• SciCrunch
• 16 years ago - by Anonymous

Java framework for building Semantic Web applications, it provides a collection of tools and Java libraries to help you to develop semantic web and linked-data apps, tools and servers. It provides extensive Java libraries for helping developers develop code that handles RDF, RDFS, RDFa, OWL and SPARQL in line with published W3C recommendations. Jena includes a rule-based inference engine to perform reasoning based on OWL and RDFS ontologies, and a variety of storage strategies to store RDF triples in memory or on disk. The Jena Framework includes: * an API for reading, processing and writing RDF data in XML, N-triples and Turtle formats; * an ontology API for handling OWL and RDFS ontologies; * a rule-based inference engine for reasoning with RDF and OWL data sources; * stores to allow large numbers of RDF triples to be efficiently stored on disk; * a query engine compliant with the latest SPARQL specification * servers to allow RDF data to be published to other applications using a variety of protocols, including SPARQL In April 2012, Jena graduated from the Apache incubator process and was approved as a top-level Apache project.

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• SciCrunch
• 17 years ago - by Anonymous

Aphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD).

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• SciCrunch
• 16 years ago - by Anonymous

Intute is a free online service that helps you to find the best web resources for your studies and research. It was created in response to users' needs and the changing Internet information environment. With millions of resources available on the Internet, it can be difficult to find useful material. The Intute subject specialists review and evaluate thousands of resources to help you choose the key websites in your subject. Intute can also help you develop your Internet research skills through our Virtual Training Suite tutorials, written by lecturers and librarians from universities across the UK. The discipline focus of their service is delivered through four new subject groups: * Science, Engineering and Technology (including geography) * Arts and Humanities * Social Sciences * Health and Life Sciences Intute is created by a consortium of seven universities, working together with a whole host of partners. The Intute consortium includes: * University of Birmingham * University of Bristol * Heriot-Watt University * The University of Manchester * Manchester Metropolitan University * University of Nottingham * University of Oxford Sponsors: Intute is funded by the Joint Information Systems Committee (JISC).

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• SciCrunch
• 17 years ago - by Anonymous

Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.

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• SciCrunch
• 13 years ago - by Anonymous

User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities.

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• SciCrunch
• 17 years ago - by Anonymous

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

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• SciCrunch
• 17 years ago - by Anonymous

The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE)

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• SciCrunch
• 17 years ago - by Anonymous

A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

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• SciCrunch
• 13 years ago - by Anonymous

Private research university in Thuwal, Saudi Arabia that offers undergraduate and graduate degree programs in Biological and Environmental Science and Engineering (BESE), Computer, Electrical, and Mathematical Science and Engineering (CEMSE), and Physical Science and Engineering (PSE).

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

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• SciCrunch
• 13 years ago - by Anonymous