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https://atcp.org/

The Ataxia Telangiectasia Children's Project, better known as the A-T Children's Project, was founded in late 1993 by a family in Florida with two young sons who have A-T. It is a public, tax-exempt, non-profit organization pursuant to Section 501(c)(3) of the Internal Revenue Code, and all gifts and donations to the Project are tax deductible. The A-T Children's Project was formed to raise funds through events and contributions from corporations, foundations and friends. These funds are then used to accelerate first-rate, international scientific research aimed at finding a cure and improving the lives of all children with ataxia-telangiectasia. - To encourage and support excellent laboratory research which will accelerate the discovery of a cure or possible therapies for ataxia-telangiectasia by: - awarding competitive research grants to top scientists using a peer-review board comprised of top scientists and physicians, - organizing and sponsoring workshops and symposiums in order to encourage cooperation among laboratories and to generate new research strategies, and - working with Congress and the National Institutes of Health to encourage the funding of active research on A-T by agencies of the U.S. government. - To improve the accurate and timely diagnosis of A-T patients by increasing public awareness and by educating physicians. - To develop and maintain an international patient registry of A-T patients with objective, neutral oversight, while leaving ultimate control in the hands of treating physicians, so that up-to-date clinical information about A-T patients can be obtained for researchers and so that when a treatment is developed, all patients can be reached through their physicians. - To support and oversee a clinical center and information clearinghouse at a top-rated, world-class medical center for the evaluation of A-T patients by a multidisciplinary team of specialists, and for the accumulation of experience in managing the many facets of A-T such as the ataxia, cancer and immune problems. - To develop quantitative endpoints for objectively measuring the progression rate and severity of the symptoms of A-T. - To maintain and enlarge a tissue/cell bank with objective, neutral oversight and control in order to ensure free access of existing and new researchers to A-T patient specimens. Sponsors: The A-T Children's Project is a non-profit organization that raises funds to support and coordinate first-rate biomedical research projects, scientific conferences and a clinical center aimed at finding a cure or life-improving therapies for ataxia-telangiectasia, a lethal genetic disease that attacks children, causing progressive loss of muscle control, immune system problems, and a strikingly high rate of cancer, especially leukemia and lymphoma.

Proper citation: Ataxia-Telangiectasia Childrens Project (RRID:SCR_001671) Copy   

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http://ahd.cbi.pku.edu.cn

Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.

Proper citation: Arabidopsis Hormone Database (RRID:SCR_001792) Copy   

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https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

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http://www.myexperiment.org/

Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

Proper citation: myExperiment (RRID:SCR_001795) Copy   

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http://www.genes2cognition.org/resources/

Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J

Proper citation: Genes to Cognition - Biological Resources (RRID:SCR_001675) Copy   

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https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

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http://www.ncbi.nlm.nih.gov/projects/homology/maps/

This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Sponsors: This resource is supported by NCBI.

Proper citation: Homology Maps Page (RRID:SCR_001666) Copy   

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http://www.mimg.ucla.edu/faculty/xing/glimmps/

Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data.

Proper citation: GLiMMPS (RRID:SCR_001787) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/SLqPCR.html

Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH.

Proper citation: SLqPCR (RRID:SCR_001669) Copy   

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https://github.com/shka/R-SAMstrt

Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package.

Proper citation: SAMstrt (RRID:SCR_001780) Copy   

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https://rgd.mcw.edu/rgdweb/portal/home.jsp?p=4

An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers.

Proper citation: Diabetes Disease Portal (RRID:SCR_001660) Copy   

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http://cmbn-approd01.uio.no/nesys/

Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.

Proper citation: Functional Anatomy of the Cerebro-Cerebellar System (FACCS) (RRID:SCR_001661) Copy   

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http://www.genesis-sim.org/GENESIS/bog/bog.html

Book with a downloadable version of the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences. Part I of the book teaches concepts in neuroscience and neural modeling by means of interactive computer tutorials on subjects ranging from neuronal membrane properties to cortical networks. These chapters, written by several contributors, allow the student to perform realistic simulations and experiments on model neural systems and provide the necessary background for understanding and using the tutorials. The simulations are user-friendly with on-line help and may be used without any prior knowledge of the GENESIS simulator or computer programming. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as students. It follows approximately the same sequence of topics as Part II, and uses parts of the tutorial simulations as examples of GENESIS programming. Several of these are based on recent research simulations which have been published in the neuroscience literature, but which have not been previously available for use outside the laboratories of the original researchers. Thus, the reader may modify these simulations and use them as a starting point for the development of original simulations. In addition to many revisions and additions to existing chapters, this second edition includes two new chapters on the modeling of biochemical signaling pathways and on the use of GENESIS on parallel computers and networks of workstations. Other new additions include a section describing ways to implement synaptic modification (learning), a section describing uses of a new method for modeling of a wide variety of voltage and ionic concentration dependent channels, a description of improvements in the procedure for implementing fast implicit numerical methods in GENESIS simulations, and descriptions of many new GENESIS commands and simulation components.

Proper citation: The Book of GENESIS (RRID:SCR_001657) Copy   

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http://www.mindandlife.org/support/mlrn/

A project of the Mind and Life Institute, fosters multidisciplinary communication about scientific research on meditation and other contemplative practices. It is dedicated to fostering dialog and research at the highest possible level between modern science and the great living contemplative traditions, especially Buddhism. It builds on a deep commitment to the power and value of both of these ways of advancing knowledge and their potential to alleviate suffering. Membership is free, and this loose affiliation of scientists, meditators, and people interested in research promotes opportunities for researchers and meditators to communicate together. All perspectives, scientific fields, and styles of meditation are welcome. The MLRN includes cognitive neuroscientists who skillfully use scientific methods in the study of meditation, meditation scholars interested in scientific interfaces, and people who can help support meditation research. MLRN members are likely to be recruited to serve as advisors, referees, participants, and collaborators in upcoming studies on meditation. The MLRN encompasses a variety of meditation practices, and incorporates both contemplative and scientific approaches. The MLRN includes a low-volume, moderated electronic announcement list. This list maintains a high signal-to-noise ratio by distributing infrequent but important messages to large numbers of recipients. Members of this announcement list receive bibliographic updates on recent publications, announcements of upcoming conferences, calls for papers for special-issue journals and conference symposia, synopses of recent meetings, announcements of relevant email lists, websites, and other resources, and other announcements appropriate for widespread distribution. Sponsors: The Hershey Family Foundation has been patron since 1990. This Institute has received generous financial support from the Fetzer Institute, The Nathan Cummings Foundation, Branco Weiss, Adam Engle, Michael Sautman, Mr. and Mrs. R. Thomas Northcote, Christine Austin, Dennis Perlman, Marilyn and the late Don Gevirtz, Michele Grennon, Klaus Hebben, Joe and Mary Ellyn Sensenbrenner, and Edwin and Adrienne Joseph.

Proper citation: MLRN (RRID:SCR_001899) Copy   

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http://www.megabionet.org/atpid/webfile/

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

Proper citation: Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) Copy   

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http://www.emory.edu/LIVING_LINKS/

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.

Proper citation: Living Links: Center for the Advanced Study of Ape and Human Evolution (RRID:SCR_001776) Copy   

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http://ipython.org

A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation.

Proper citation: IPython (RRID:SCR_001658) Copy   

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https://www.ku.ac.th/th/community-home

Public university in the capital of Thailand. Originally created to promote agricultural sciences, it now offers degrees in a range of fields including engineering, social sciences, business administration, and education.

Proper citation: Kasetsart University; Bangkok; Thailand (RRID:SCR_001659) Copy   

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https://sbpdiscovery.org/tag/neuroscienceandagingresearchcenter/

Center that translates basic science discoveries into new treatments to extend lifespan and to combat degenerative disorders associated with aging or development. Their researchers are discovering the etiological pathways as well as small-molecule and stem cell-based treatments to address the clinical unmet need of these patients. The Center uses a team based approach to apply their expertise in stem cells to develop therapies for new treatments for stroke and Parkinson's disease. They are also performing high-throughput screens to identify new molecules to protect the synapses of nervesthe connections between nerves that mediate movement, memory and cognition for Alzheimer's, Parkinson's and autism. By studying the links between Down syndrome and Alzheimer's disease, they are exploring new treatments to improve cognition in both disorders. Their collaborations with clinical partners enable them to test new discoveries in human trials, with a goal to improve the lives of patients and families affected by neurodegenerative disease and aging disorders.

Proper citation: Sanford-Burnham Neuroscience and Aging Research Center (RRID:SCR_001688) Copy   

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http://www.archive.org/

An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

Proper citation: Internet Archive (RRID:SCR_001682) Copy   

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