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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
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
http://www.medicalnumerics.com/products/medx/index.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 06, 2013. Per the associated paper, Aguirre GK (2012) FIASCO, VoxBo, and MEDx: behind the code. Neuroimage 62: 765-7, the MedX software was discontinued. The website itself however, looks like you can still buy it (website last updated 2004). Highly optimized, portable, commercial software for the visualization, processing, and analysis of medical images. The packages include: SPM '99, FSL, DICOM Import/Export, ABLe, Functional Data Simulator. Designed especially for medical imaging researchers and system developers, MEDx brings multi-modality, multi-dimensional image processing functionality to the medical imaging research community. With MEDx, users display images and control menus using the industry-standard XWindow display system and Tcl/Tk interface language. MEDx transforms your computer into a powerful image processing workstation that displays, analyzes, and processes your medical image data in a myriad of innovative ways.
Proper citation: MEDx (RRID:SCR_002023) Copy
The Parkinsons Disease Society funds research, offers educational information, advice, and support from medical professionals, and runs campaigns with the goal of offering support, raising money, and finding a cure for Parkinsons disease. In addition to funding research, the Society offers a Helpline to support those suffering from Parkinsons and their caregivers, and also offers a range educational materials. The Society has a network of over 330 branches and support groups located across the UK. Additionally, the Society campaigns for and influences government policy and the development of high-quality services at a local and national level.
Proper citation: Parkinsons UK (RRID:SCR_002022) Copy
PASS is a computer program which predicts the biological activity spectrum for a compound on the basis of its structural formula. The result of prediction is displayed for free. PASS Inet predicts 3678 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, teratogenicity and embryotoxicity. PASS gives you hits in the following: - Finding most probable new leads with required activity spectra among the compounds from in-house and commercial data bases. - Revealing new effects and mechanisms of action for the old substances in corporate and private data bases. - Providing the basis for selection of the most prospective compounds for high throughput screening from the set of available samples. - Determining the assays that are more relevant for a particular compound. Sponsors: This work is supported by the Russian Foundation for Basic Research (Grant # 03-07-90282).
Proper citation: Prediction of Activity Spectra for Substances (RRID:SCR_001971) Copy
The mission of the National Parkinson Foundation is to improve the quality of care for people with Parkinson's disease through research, education and outreach. NPF funds research through four main programs: the Centers of Excellence Network, which focuses on clinical studies of new therapeutic approaches; the Parkinson's Outcomes Project, a large clinical study of Parkinson's disease; the Grants/Clinical Research Fund, which provides funding to individual researchers; and fellowship awards, which are used to train neurologists in the movement disorder specialty.
Proper citation: National Parkinson Foundation (RRID:SCR_002017) Copy
http://www.nitrc.org/projects/itk-snap/
Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
Proper citation: ITK-SNAP (RRID:SCR_002010) Copy
http://cvlab.epfl.ch/NeuroMorph
A toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks. It is designed to import, analyze, and visualize mesh models. It has been designed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, although much of its functionality can be applied to any 3D mesh. These models can be generated by software that allows the images to be segmented so that 3D objects can be built. These objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. The NeuroMorph toolset has been developed as a set of add-ons for Blender, a widely used free and open source 3D modeling software package.
Proper citation: NeuroMorph (RRID:SCR_002091) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowTrans.html
Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.
Proper citation: flowTrans (RRID:SCR_002093) Copy
https://github.com/trendscenter/gift
Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki.
Proper citation: Group ICA of fMRI Toolbox (RRID:SCR_001953) Copy
Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.
Proper citation: Rat Resource and Research Center (RRID:SCR_002044) Copy
Desktop software suite targeted to curators and experimentalists that assists in the reporting and local management of experimental metadata, engages with minimum information checklists and ontologies and formats studies for submission to international public repositories. The ISA software suite is the product of an ongoing collaboration between various research and service groups from diverse life science domains. It represents an opportunity for the wider research community to start taking data management into their own hands by supporting graduated adherence to community standards and the efficient curation of experimental metadata at source, shielded from underlying complexities. The software suite is comprised of several platform-independent Java-based software components for local use, including a relational database, built around the ISA-Tab format. The components work both as stand-alone applications and as a unified system.
Proper citation: ISA Infrastructure for Managing Experimental Metadata (RRID:SCR_002041) Copy
Society of Radiologic Technologists to advance the medical imaging and radiation therapy profession and to enhance the quality of patient care, leading and serving its members, the profession, other health care providers and the public on all issues that affect the radiologic sciences. The mission of the ASRT is to foster the professional growth of radiologic technologists by expanding knowledge through education, research and analysis; promoting exceptional leadership and service; and developing the radiologic technology community through shared ethics and values. This portal offers information on Continuing Education opportunities, and has a variety of other resources including a marketplace, news, publications, events and conferences, career center, studies and surveys, professional resources, and much more. Scholarly Journals Members can earn CE credit through the Directed Readings program in the ASRT journals, Radiologic Technology and Radiation Therapist. By maintaining continuous membership, members can earn at least 12 Category A CE credits. Answer sheets for Directed Reading Quizzes can be completed on our Web site or mailed to the ASRT for grading. You will receive pass or fail notification immediately on the Web site or ASRT will notify you within 30 days if your completed quiz is mailed. A passing grade of 75 percent or better is required to receive the assigned Category A credit.
Proper citation: American Society of Radiologic Technologists (RRID:SCR_001984) Copy
https://www.bbe.caltech.edu/academics/cns
Portal offers information on people, research, seminars, academics, admissions, positions, and news, associated with interdisciplinary program to study problems arising at interface between neurobiology, electrical engineering, computer science, and physics. Applicants for Graduate Admissions should have undergraduate major in electrical engineering, biology, physics, mathematics, or computer science, and general background that will permit enrolling in advanced courses in other relevant disciplines. Admitted students will become affiliated with one of three participating divisions as appropriate to their background and interests. Post-doc positions are also available.
Proper citation: California Institute of Technology - Computation and Neural Systems (RRID:SCR_001985) Copy
https://github.com/nicolazzie/AffyPipe
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
Proper citation: AffyPipe (RRID:SCR_002032) Copy
Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.
Proper citation: Addgene (RRID:SCR_002037) Copy
https://github.com/adrlar/CanSNPer
Software that is a hierarchical genotype classifier of clonal pathogens.
Proper citation: CanSNPer (RRID:SCR_001980) Copy
Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.
Proper citation: Candida Genome Database (RRID:SCR_002036) Copy
http://sourceforge.net/projects/dmetanalyzer/
Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.
Proper citation: DMET-Analyzer (RRID:SCR_002030) Copy
http://biodev.extra.cea.fr/interoporc/
Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.
Proper citation: InteroPorc (RRID:SCR_002067) Copy
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