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http://www.neurogems.org/neosim/

Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows

Proper citation: Neural Open Simulation (RRID:SCR_002916) Copy   

•   Source: SciCrunch Registry

http://cbio.mskcc.org/

Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling

Proper citation: Computational Biology Center (RRID:SCR_002877) Copy   

•   Source: SciCrunch Registry

http://www.mct.gov.br/index.php/content/view/323883.html

Proper citation: Brazilian Ministry of Science Technology and Innovation (RRID:SCR_002876) Copy   

•   Source: SciCrunch Registry

https://github.com/nichtich/marginalia/wiki/Support-of-PDF-annotations

Wiki that provides a listing (and associated links) of various formats to store and export annotations. Apparently everyone uses his own proprietary format to store and export annotations. The FDF format (or better its XML variant XFDF) is or was used by Acrobat to store form values and annotations, but third-party implementations focus on the forms-part of FDF instead of the annotations-part. * XML Forms Data Format Specification (XFDF) 2.0 (2007). * iText classes (no full FDF/XFDF implementation) ** FdfReader ** FdfWriter ** XfdfReader * The commercial software Adobe Digital Editions explicitly supports external annotations. The FAQ says Digital Editions supports bookmarks, highlights, and text notes via its bookmarks panel. These annotations are stored in an open XML format separately from publications to enable seamless annotation across PDF- and EPUB-based publications. They will set the stage for future social networking features (such as sharing annotations within a community of readers). * Okular has its own annotation exchange format, similar to PDF annotation (comparison is needed) ** internal API documentation ** There is no file format documentation, but the source code is mainly in the methods AnnotationUtils storeAnnotation and Annotation store * Xournal is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations * Mendeley supports annotations, which can be synced independent from the PDF files they refer to, and exported together with PDFs. There is no documentation of the API and format they use to exchange annotations. * Evernote is worth a view. But proprietary and no Linux client. * iAnnotate seems to be popular on the iPad - can it export and import annotations? In which format? There is a good article by Scott McLeod with screenshots about his use of iAnnotate and Evernote to take notes (June 15, 2010). http://blogs.edweek.org/edweek/LeaderTalk/2010/06/tools_for_school_digital_docum.html

Proper citation: Support-of-PDF-annotations (RRID:SCR_002871) Copy   

•   Source: SciCrunch Registry

http://www.iscos.org.uk

ISCoS promotes the highest standard of care in the practice of spinal cord injury for men, women and children throughout the world. Through its medical and multi disciplinary team of Professionals ISCoS endeavours to foster education, research and clinical excellence. ISCoS has a membership of over 1,000 Clinicians and Scientists from 87 countries. They regularly update their knowledge at the Annual Scientific Meeting held in a different country each year. Goals of ISCoS: :- Serve as an international impartial, non-political and non-profit making association whose purpose is to study all problems relating to traumatic and non-traumatic lesions of the spinal cord. This includes causes, prevention, basic and clinical research, medical and surgical management, clinical practice, education, rehabilitation and social reintegration. This society will function in close collaboration with other national and international bodies, thereby encouraging the most efficient use of available resources. :- Provide a scientific exchange among its members and others by collecting and disseminating information through publications, correspondence, exhibits, regional and international seminars, symposia, conferences and otherwise. :- Advise, encourage, promote and when requested, assist in efforts to co-ordinate or guide research, development and evaluation activities related to spinal cord lesions throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the care of patients involved and when requested, correlate these activities throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the education and training of medical professionals and professionals allied to medicine and when requested, correlate these activities throughout the world.

Proper citation: International Spinal Cord Society (RRID:SCR_002908) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/lovd/home.php?select_db=OCRL

The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics

Proper citation: Lowes Syndrome Mutation Database (RRID:SCR_002907) Copy   

•   Source: SciCrunch Registry

http://www.bhf.org.uk/

British charity and fundraiser for cardiovascular research.

Proper citation: British Heart Foundation (RRID:SCR_002905) Copy   

•   Source: SciCrunch Registry

http://www.ouhsc.edu/compmed/documents/DevelopmentofaSpecificPathogenFreeBaboonColony.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals.

Proper citation: Development of a Specific-Pathogen-Free Baboon Colony (RRID:SCR_002900) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/tuschl/

RNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes.

Proper citation: Tuschl Laboratory: RNA Molecular Biology (RRID:SCR_002866) Copy   

•   Source: SciCrunch Registry

https://uni-koeln.de/

Public university in Germany that offers degrees in law, management and business, the arts and humanities, and human sciences.

Proper citation: University of Cologne; Cologne; Germany (RRID:SCR_002903) Copy   

•   Source: SciCrunch Registry

http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl

Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.

Proper citation: Patterns of Gene Expression in Drosophila Embryogenesis (RRID:SCR_002868) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/CNVassoc/

Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

Proper citation: CNVassoc (RRID:SCR_002901) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiHome.html

The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. It provides users the tools to BLAST search, browse genome regions (to retrieve DNA, find clones, and graphically view sequence regions), and provides gene indexes and genome statistics. We were funded to attempt 7x sequence coverage comprising paired end reads from plasmids, Fosmids and BACs. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Our specific aims are as follows: 1. Generate and assemble sequence reads yielding 7X coverage of the Magnaporthe oryzae genome through whole genome shotgun sequencing. 2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end of average every 2 kb. 3. Integrate the genome sequence with existing physical and genetic map information. 4. Perform automated annotation of the sequence assembly. 5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server and by deposition of the sequence assembly in GenBank.

Proper citation: Magnaporthe comparative Database (RRID:SCR_003079) Copy   

•   Source: SciCrunch Registry

http://studyforrest.org

An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

Proper citation: studyforrest.org (RRID:SCR_003112) Copy   

•   Source: SciCrunch Registry

http://www.bioconferencelive.com/

Online conferences focused on the life sciences, laboratory animal sciences and clinical diagnostics community. BioConference Live brings together research scientists, veterinarians, clinicians, medical experts, thought leaders and professionals from around the world all exclusively online. * Receive CE Credits accredited by the AACC ACCENT and PACE. * No Cost or Travel. * Watch Live Streaming Sessions by Industry Experts. * Network with peers and professionals. * Explore a virtual exhibit floor showcasing advances in life sciences and medical technologies.

Proper citation: BioConference Live (RRID:SCR_003110) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.

Proper citation: SciCrunch (RRID:SCR_003115) Copy   

•   Source: SciCrunch Registry

http://colorado.edu/

Public university that offers degrees in the sciences, humanities, and social sciences.

Proper citation: University of Colorado Boulder; Colorado; USA (RRID:SCR_003114) Copy   

•   Source: SciCrunch Registry

http://chiulab.ucsf.edu/surpi/

Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Proper citation: SURPI (RRID:SCR_003071) Copy   

•   Source: SciCrunch Registry

http://www.fly-trap.org/

Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.

Proper citation: flytrap (RRID:SCR_003075) Copy   

•   Source: SciCrunch Registry

http://www2.niddk.nih.gov/Research/Resources/ObesityResources.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 23, 2017. This website contains resources for obesity researchers including: Obesity Databases, Registries and Information; Obesity Multicenter Clinical Research; Obesity Basic Research Networks; Obesity Reagents; Obesity Services; Obesity Standardization Programs; Obesity Tissues, Cells, Animals; Obesity Useful Tools.

Proper citation: NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources (RRID:SCR_003074) Copy   

•   Source: SciCrunch Registry