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http://medschool.umaryland.edu/btbank/
The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.
Proper citation: NICHD Brain and Tissue Bank for Developmental Disorders (RRID:SCR_003601) Copy
Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances.
Proper citation: GOCat (RRID:SCR_003608) Copy
http://www.alsace-biovalley.com/en/
A French world-class cluster dedicated to therapeutic innovations, it is the one-stop contact to optimize any R&D development or business project in Europe, both in drug development and medical technologies. Located in Alsace region, part of the famous French-German-Swiss BioValley and with a unique concentration of international life sciences & healthcare players, Alsace BioValley helps any Life Sciences & Healthcare companies interested in new projects and partnerships in Europe: * to search outstanding scientific or industrial partners to develop very innovative R&D projects * to find the best innovative technology, patent or scientific expertise * to set up and locate in Alsace region
Proper citation: Alsace BioValley (RRID:SCR_003729) Copy
https://github.com/distrep/DMLT
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A machine learning toolbox written in Matlab and C that provides a general interface to support the integration of new statistical machine learning methods by writing high level wrappers. It allows complex methods to be built from simple building blocks and makes the use of cross-validation and permutation testing as easy as writing one line of Matlab code. The code requires at least Matlab distribution 7.6.0.324 (R2008a).
Proper citation: Donders Machine Learning Toolbox (RRID:SCR_003561) Copy
https://github.com/automaticanalysis/automaticanalysis
Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.
Proper citation: Automatic Analysis (RRID:SCR_003560) Copy
A collaboration to test an adaptive clinical trial model that would assess the efficacy of a candidate therapeutic earlier than traditional clinical trials, potentially enabling drugs to be developed and approved using fewer patients, less time and fewer resources. This trial focuses on women with newly diagnosed locally advanced breast cancer to test whether adding investigational drugs to standard chemotherapy is better than standard chemotherapy alone. It uses genetic and biological markers from individual patients' tumors to screen several promising new treatments simultaneously and allows doctors to quickly measure the effectiveness of the treatment prior to removing the tumor. The experimental adaptive trial design uses patient outcomes to immediately inform treatment options for subsequent trial participants. The trial has 5 components that differentiate it from conventional clinical trial models. # I-SPY2 uses tissue and imaging biomarkers from individual cancer patients' tumors to determine eligibility, guide/screen promising new treatments and identify which treatments are most effective in specific tumor subtypes. # The trial's adaptive design allows the Team to learn as they go, enabling researchers to use data from patients early in the trial to guide decisions about which treatments might be more useful for patients who enter the trial earlier. I-SPY2 provides a scientific basis for researchers to eliminate ineffective treatments and graduate effective treatments more quickly. # The neoadjuvant treatment approach - in which chemotherapy is given to patients prior to surgery - allow the team to evaluate tumor response with MRI before removal. This approach is safe as treating after surgery, allowing tumors to shrink, and more importantly, it enables critical learning early on about how well treatments work. # The ability for the team to screen multiple drug candidates developed by multiple companies. New agents will be selected and added as those used initially and either graduate to Phase III, or are dropped, based on their efficacy in targeted patients. # The trials informatics system allows data to be collected, verified, and shared in real-time. This allows data to be assessed early and in an integrated fashion - with an aim to enhance and encourage collaboration
Proper citation: I-SPY 2 TRIAL (RRID:SCR_003713) Copy
Project to develop a drug safety database from the pharmaceutical industry legacy toxicology reports and public toxicology data; innovative in silico strategies and novel software tools to better predict the toxicological profiles of small molecules in early stages of the drug development pipeline. The project is creating this pharmaco-toxicological database with an aim to: * Reduce the number of animal tests * Decrease the attrition rates of new drug candidates * Increase the success rate of new molecular entities becoming drugs * Improve the safety of drugs on the market The project consists of three different systems, * eTOX VITIC Database a unified database containing all confidential and non-confidential data collected in eTOX (historical data from the pharmaceutical industry) * ChOX Database a unified database containing public data (literature and public database) * eTOXsys Query and Prediction System an interface providing a uniform access to the two databases (VITIC and ChOX) and to all developed prediction models and systems
Proper citation: eTOX (RRID:SCR_003712) Copy
Consortium to identify, fund and support breakthrough technologies that will significantly enhance biopharmaceutical R&D productivity and accelerate the development of new safe and efficacious drugs. CQDM is a neutral ground that brings patient groups, academia, governments, biotech and the pharma industry together to work collaboratively on complex medical challenges. Projects supported by the consortium are highly relevant to the pharmaceutical sector and typically address: * Opportunity for new therapeutic approaches and research * Safe and effective new drug development * Enhancing the efficacy of already existing drugs * Reducing costs, time and risks associated with the discovery and development of new drugs Funded projects typically involve multidisciplinary collaborations between research teams that represent both the academic and the private sector, who are mentored by industry scientists provided by the consortium sponsors.
Proper citation: Quebec Consortium for Drug Discovery (RRID:SCR_003711) Copy
Consortium aiming to improve pancreatic beta-cell function and identification of diagnostic biomarkers for treatment monitoring in diabetes. It brings together academic teams, pharmaceutical companies, and a Small to Medium Enterprises (SMEs), which provides a unique blend of expertise and forms a strong basis for a successful enterprise to ultimately improve industrial competitiveness and Public Health in Europe. The program aims at delivering: * Novel tools for the study of human beta-cell development, function and survival; their modulation by potential therapeutic compounds; and for in vivo beta-cell imaging. * Biomarkers for the diagnosis and prognosis of beta-cell failure and for monitoring diabetes progression and treatment. * Knowledge on novel molecular pathways and sites that control beta-cell life & death as well as mass and function.
Proper citation: IMIDIA (RRID:SCR_003865) Copy
A non-profit network of allergy, asthma and Chronic Obstructive Pulmonary Disease (COPD) patients' organisations, representing 35 national associations in 22 countries and over 400,000 patients. They're dedicated to making Europe a place where people with allergies, asthma and COPD have the best quality care and a safe environment, live uncompromised lives and are actively involved in all decisions influencing their health. They work on behalf of patients to: * Promote awareness of allergies and airways diseases among policymakers and the general public. * Broaden our understanding of these conditions by increased collaboration between national patient associations. * Share knowledge and experience to beneficially educate both the public and EFA members. * Promote patient concerns and opinions within the European institutions and enable national patient associations to gain representation at EU level. * Improve their health and quality of life.
Proper citation: European Federation of Allergy and Airways Diseases Patients Associations (RRID:SCR_003855) Copy
Consortium working to advance the development of potential antibiotics against Gram-negative bacteria, such as Escherichia coli. The project creates and manages a drug discovery engine for testing and optimizing molecules that are still in the earlier stages of drug discovery but have the potential to become future drug candidates capable of treating resistant Gram-negative infections. The project will focus on the discovery and pre-clinical stages of drug development, as well as (potentially) phase 1 clinical trials. ENABLE will run several drug discovery programs in parallel and the consortium seeks external hit and lead programs to join, through a series of open calls during the project. Researchers who have interesting molecules will have the opportunity to collaborate with a diverse range of experts in microbiology, pharmacology and chemistry to help advance their molecule through the drug development process until it is an attractive candidate for clinical testing. Specifically, the project is working towards: # identifying three antibacterial lead molecules which, following extensive testing, have been identified as having promising antimicrobial activity; # identifying two antibacterial clinical candidate molecules # advancing at least one compound into preclinical and phase 1 clinical studies, i.e. early clinical safety testing in humans.
Proper citation: European Gram Negative AntiBacterial Engine (RRID:SCR_003859) Copy
https://www.europeanleadfactory.eu/
Consortium that promotes the discovery of novel small molecule candidates suitable for subsequent optimization either to drug candidates or to high-quality pharmacological tools for the experimental validation of targets using open innovation and crowd sourcing. It is designed to provide best-in-class resources and funding-in-kind, to academics or small and medium enterprises (SMEs) who are working on promising biology targets or chemistry scaffolds. Screening of compounds to assess their activity is also funded and performed by the EU Lead Factory, with collaboration to help develop an Improved Hit List from the Qualified Hit List. They will provide collaborative screening of previously safeguarded, high quality corporate compounds. Around 300,000 compounds in the EFPIA Compound Collection, contributed by EFPIA members, will be screened against both commercially contributed biology targets and targets from public sources. The second phase of the consortium is to build a substantial new Public Compound Collection of around 200,000 compounds. Together, the EFPIA and Public compound collections will form a 500,000-strong Joint European Compound Collection. Target program owners and compound contributors will receive a Qualified Hit List (QHL) of up to 50 compounds complete with relevant information to help in the development of an Improved Hit List (IHL). Target program owners, will have exclusive access to threshold active compounds in their QHL. After the three-year exclusivity period, QHL/IHL information will be made public. Milestone payments are due if direct exploitation proceeds, not for research use. And owners and contributors will give EFPIA participants the right to submit a first bid (which they do not have to accept).
Proper citation: European Lead Factory (RRID:SCR_003858) Copy
Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.
Proper citation: Structural Genomics Consortium (RRID:SCR_003890) Copy
http://fcon_1000.projects.nitrc.org/indi/CoRR/html/
Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans
Proper citation: Consortium for Reliability and Reproducibility (RRID:SCR_003774) Copy
An Antibody supplier
Proper citation: Primm Biotech (RRID:SCR_003809) Copy
http://www.alzheimer-europe.org/
A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia.
Proper citation: Alzheimer Europe (RRID:SCR_003802) Copy
Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies.
Proper citation: NeuroVault (RRID:SCR_003806) Copy
A question answering web site and forum that focuses on neuroinformatics and neuroscience. Initially conceived by Istvan Albert's highly successful BioStar website within the Bioinformatics community, NeuroStars is born as an experiment to engage the Neuroinformatics community after some unfruitful attempts in StackExchange's Area51. Posts that are detailed and specific, written clearly and simply are welcome.
Proper citation: NeuroStars (RRID:SCR_003805) Copy
An on-demand archiving system for webreferences (cited webpages and websites, or other kinds of Internet-accessible digital objects), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future. Users make a local copy of the cited webpage / webmaterial and archive the cited URL to enable readers permanent access to the cited material. If cited webreferences in journal articles, books etc. are not archived, future readers may encounter a 404 File Not Found error when clicking on a cited URL. It's free and takes only 30 seconds. A WebCite-enhanced reference is a reference which contains - in addition to the original live URL (which can and probably will disappear in the future, or its content may change) - a link to an archived copy of the material, exactly as the citing author saw it when he accessed the cited material.
Proper citation: WebCite (RRID:SCR_003804) Copy
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