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Consortium to accelerate new breakthrough DNA sequencing technologies and methods to enhance existing analysis methods. The ultimate aim is to advance DNA sequencing technologies to a level where a human genome can be analyzed at high resolution for less than 1000 euros in less than one day. The goals of the consortium are to revolutionize nucleic acid analysis methods by improving elements necessary to use the currently emerging generation of nucleic acid sequencers in a meaningful and accessible way, providing methods that allow in situ nucleic acid analysis and methods capable of selectively characterizing mutant DNA in a high background of wildtype DNA, combining RNA and DNA analysis in a single analytical device, providing technology to efficiently analyze DNA methylation (genome-wide, with high resolution and in its long-range context), implementing novel concepts for high-throughput HLA-screening, developing fully integrated solutions for mutational screening of small target regions (such as for screening newborns for cystic fibrosis mutations), developing a device for screening multiple target regions with high accuracy and implementing strategies for effective and high-resolution genotyping of copy number variations. READNA was awarded the Stars of Europe prize in December 2013.
Proper citation: READNA (RRID:SCR_003884) Copy
Project that aims to increase understanding of how orally-administered drugs are taken up from the gastrointestinal tract into the body, and apply this knowledge to create new laboratory tests and computer models that will better predict the performance of these drugs in patients over a range of clinically relevant conditions. The integration of in vitro and in silico approaches will provide a biopharmaceutics toolkit, validated using clinical data, to accelerate drug development. Ultimately, the project will help to facilitate and speed up the formulation development process and significantly reduce the need for animal experiments in this area as well as for human clinical studies in the future. For patients, the main benefit will be in the form of high quality medicines where the dose required is well calculated and is released in a way that consistently provides an optimal clinical effect.
Proper citation: ORBITO (RRID:SCR_003876) Copy
A computationally-oriented biotech company located in Barcelona that is focused on the drug discovery and development areas. Chemotargets' goal is to help the biopharma industry fast-forward the process of bringing new medicines to market, speeding up drug discovery and development programs and making them more cost-efficient. To this end, they have designed, and continue to develop, an integrated technology platform involving a broad spectrum of cutting-edge computational methodologies.
Proper citation: Chemotargets (RRID:SCR_003793) Copy
A non-governmental, non-profit public database for paleontological data providing researchers and the public with information about the entire fossil record. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database's broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions. Paleontological data files are accepted for upload. However, PaleoBioDB needs some basic data types to be included in order to perform an upload. The Application Programming Interface (API) gives scientists, students, and developers programmatic access to taxonomic, spatial, and temporal data contained within the database.
Proper citation: Paleobiology Database (RRID:SCR_003798) Copy
Project targeting vulnerable plaques causing unexpected acute myocardial infarcts and sudden cardiac deaths by identifying and validating novel drug targets as well as devising and validating diagnostic tests. It has been designed to advance the present knowledge on the role of inflammatory remodeling in the different stages of atherosclerosis. It will also provide important knowledge for the development of strategies for prevention and clinical management of vascular diseases.
Proper citation: AtheroRemo (RRID:SCR_003831) Copy
An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.
Proper citation: Jmol (RRID:SCR_003796) Copy
https://www.biogen.com/en_us/home.html
Global biotechnology company based in Cambridge, Massachusetts, specializing in discovering, developing, and delivering important therapies for the treatment of neurodegenerative, hematologic and autoimmune diseases to patients worldwide.
Proper citation: Biogen Idec (RRID:SCR_003790) Copy
Organization that drives the development of disease-modifying treatments against Alzheimer's, Parkinson's, Diabetes and other protein misfolding disorders through two independently managed business units: * Contract Research: The in-vivo Contract Research Organization (CRO) helps its clients to assess the pharmacokinetics and -dynamics of their experimental treatments against Alzheimer's disease. The main focus is on efficacy testing of candidate drugs in reMYND's proprietary Alzheimer mouse models expressing the clinical APP-London allele as single transgene or in combination with clinical alleles of human PS1 and TAU. * Drug Discovery: The Drug Discovery and Development Unit (DDD) focuses on disease-modifying treatments against protein-misfolding disorders, such as Alzheimer's disease (tau), Parkinson's disease (-synuclein), and Diabetes. In addition, reMYND grants licenses and markets commercial kits of RadarScreen, a technology for rapid and cost-effective identification of genotoxic liabilities in early stage drug discovery. reMYND has been substantially supported by grants from IWT and from The Michael J Fox Foundation.
Proper citation: reMYND (RRID:SCR_003824) Copy
A bio-pharmaceutical company with a focus on research and development of new targets & therapies against proliferative diseases. Its current development program is based on inecalcitol, a vitamin D receptor agonist being studied in three potential indications: * alone in chronic lymphocytic leukaemia * in combination with imatinib in chronic myeloid leukaemia * in prostate cancer, for use with current standards of care Hybrigenics'' research program investigates the action of enzymes called Deubiquitinating Enzymes (DUBs) in the recycling of onco-proteins and the utility of proprietary patented DUB inhibitors against various cancer indications. Hybrigenics Services, a Hybrigenics subsidiary, markets very specialized scientific services to researchers in all areas of life sciences who want to identify, validate and inhibit protein interactions in animal, plant or microbiological cells.
Proper citation: Hybrigenics (RRID:SCR_003822) Copy
Foldit is a revolutionary new multiplayer online computer game that engages non-scientists in solving hard prediction problems, enabling you to contribute to important scientific research. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. Here are the basic principles to keep in mind when folding proteins. Your score on each protein is based on how well you do with these three things: # Pack the protein: The smaller the protein, the better. More precisely, you want to avoid empty spaces (voids) in the structure of the protein where water molecules can get inside. So you want the atoms in the protein to be as close together as possible. Certain structures, such as sheets, will even connect together with hydrogen bonds if you line them up right and get them close together. This is also good. Key word: Compact. # Hide the hydrophobics: Hydrophobics are the sidechains that don't want to be touching water, just like oil or wax. Since most proteins float around in water, you want to keep the hydrophobics (orange sidechains) surrounded by as many atoms as possible so the water won't get to them. The other side of this rule is that hydrophilics (blue sidechains) do want to be touching water, so they should be exposed as much as possible. Key word: Buried. # Clear the clashes: Two atoms can't occupy the same space at the same time. If you've folded a protein so two sidechains are too close together, your score will go down a lot. This is represented by a red spiky ball (clash) where the two sidechains are intersecting. If there are clashes, you know something is wrong with your protein. So make sure everything is far enough apart. Key word: Apart. The current series of Science Puzzles, the Grand Challenges, are meant to generate the evidence needed to prove that human protein folders can be more effective than computers at certain aspects of protein structure prediction. That's what all the puzzles in Foldit are about right now: predicting the structure of a protein based on its amino acid sequence. The three rules mentioned above describe the characteristics of correct protein structures.
Proper citation: Foldit (RRID:SCR_003788) Copy
Private research university in Rochester, New York. University grants undergraduate and graduate degrees, including doctoral and professional degrees.
Proper citation: University of Rochester; New York; USA (RRID:SCR_003821) Copy
Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc.
Proper citation: Amorfix (RRID:SCR_003783) Copy
http://www.patientslikeme.com/
A for-profit health data-sharing platform that can transform the way patients manage their conditions, change the way industry conducts research and improve patient care. PatientsLikeMe aligns patient and industry interests through data-sharing partnerships. They work with trusted nonprofit, research and industry Partners who use this health data to improve products, services and care for patients. They take the information patients share about their experience with the disease and sell it to their partners (i.e., companies that are developing or selling products to patients). These products may include drugs, devices, equipment, insurance, and medical services. Except for the restricted personal information entered when registering for the site, participants should expect that every piece of information submitted (even if it is not currently displayed) may be shared with their partners and any member of PatientsLikeMe, including other patients. They do not rent, sell or share personally identifiable information for marketing purposes or without explicit consent. Because they believe in transparency, they tell members exactly what they do and do not do with their data. Patients have the opportunity to share both personal stories and health data about their conditions to help uncover great ideas and new knowledge. By sharing information on the site, they can put their disease experiences in context and find answers to the questions they have. Every partnership we develop must bring them closer to aligning patient and industry interests. Their end goal is improved patient care and quality of life.
Proper citation: PatientsLikeMe (RRID:SCR_003781) Copy
http://www.innomed-addneuromed.com/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.
Proper citation: AddNeuroMed (RRID:SCR_003819) Copy
Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University.
Proper citation: MRC Cognition and Brain Sciences Unit (RRID:SCR_003818) Copy
A human writeable and human readable language to express the information required to describe pharmacometric models and tasks using these models. The specification of the MDL offers a standard for coding models and associated objects and defining how to execute tasks. The standards for defining MDL objects are independent of any specific target modelling software. This allows the user to specify the model in a consistent manner and facilitates understanding of the model and associated tasks, regardless of the software used to build the model. New modelling applications may take advantage of the standard without having to re-invent how to describe common modelling processes.
Proper citation: MDL (RRID:SCR_003816) Copy
Commercial organization that manufactures Vacuum Electron Devices and Associated RF Circuits for Communications, Science, Radar, Industry & Directed Energy Applications. Other products include photo-detectors for scientific and medical applications and specialized material processing and plating services.
Proper citation: PHOTONIS (RRID:SCR_003853) Copy
http://www.blueprint-epigenome.eu/
Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system.
Proper citation: Blueprint Epigenome (RRID:SCR_003844) Copy
A European public-private consortium examining ways to make chemical research and the pharmaceutical industry more sustainable and environmentally friendly with the aim of developing sustainable biological and chemical alternatives to finite materials, such as precious metals, which are currently used as catalysts in the manufacture of medicines. The project has looked at the industry and identified needs and barriers, and is now working to develop methods to navigate around them to reduce costs for companies and thus reduce prices for patients. Chem21 also involves an educational training component that will help instill the project's results in the next wave of scientists. The project has four focus areas that are driving it toward the desired impact on the 21st century pharmaceuticals industry: * New, more efficient catalyst classes made available for greening processes and the generation of novel molecules * Alternative methodologies clearly described to allow broader use * New modified microorganisms for preparing pharma building blocks disclosed * Training materials developed for driving longer-term innovation
Proper citation: CHEM21 (RRID:SCR_003848) Copy
http://www.europeanlung.org/en/
Foundation with aim of bringing together patients, the public and respiratory professionals to positively influence lung health and respiratory medicine. ELF aims to communicate respiratory science to those outside of the respiratory field, to ensure that people with lung diseases and the general public have a chance to influence respiratory research and guidelines at a European level.
Proper citation: European Lung Foundation (RRID:SCR_003842) Copy
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