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http://www.globalhealthlibrary.net/php/index.php
The Global Health Library assembles health data, readable in many languages. The GHL aims to: * point to reliable information collections and systems, in which different users and user groups (ministries of health, policy makers, health workers, information providers, patients and their families, general public) can focus on the knowledge that best meets their health information needs; * act as a facilitator enabling access to information contents produced by numerous key providers - be they commercial companies, government institutions, civil society, not-for-profit organizations, and regional or international bodies; and * strive for universality, with focus on developing countries, and will act as a resource locator for print materials essential to areas that do not have access to electronic content.
Proper citation: World Health Organization: The Global Health Library (RRID:SCR_000391) Copy
A collection of both commercial and noncommercial software products which includes: Mascot Distiller, Mascot Parser, and Mascot Server. Mascot Distiller is commercial and provides a single interface to process raw data into de-isotoped peak lists. This tool can also be used for the easy distribution of search and quantitative results to colleagues. The non-commercial Mascot Parser software provides an API (Application Programmer Interface) that makes it easier to access search results written in C++, Java, Python and Perl. Mascot Server is non-commercial, and is a collection of peptide mass fingerprints as well as a MS/MS database. A selection of popular sequence databases are available online and include SwissProt, NCBInr, and the EST divisions of EMBL. This server is best used for evaluating and searching for smaller data sets.
Proper citation: MatrixScience (RRID:SCR_000307) Copy
Database platform that aggregates post-publication peer reviews and ratings. It also includes a large-scale bibliographic database and features free reference management tools.
Proper citation: Epistemio (RRID:SCR_000429) Copy
A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
Proper citation: PyMOL (RRID:SCR_000305) Copy
http://sourceforge.net/projects/limsforproteomi/
Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.
Proper citation: LIPAGE (RRID:SCR_000290) Copy
https://github.com/johnomics/RADtools
Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers.
Proper citation: RADtools (RRID:SCR_000324) Copy
https://sites.google.com/site/emesbioinformatics/group-software/nimbl
MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.
Proper citation: NIMBL (RRID:SCR_000482) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.
Proper citation: Simulx (RRID:SCR_000486) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.
Proper citation: PharmML (RRID:SCR_000487) Copy
A nonprofit health organization that works to improve the quality of life of Canadians affected by Alzheimer's disease and other dementias. This organization also supports research on the cause and potential cures for the disease through education and funding.
Proper citation: Alzheimer Society of Canada (RRID:SCR_000485) Copy
https://github.com/information-artifact-ontology/IAO
An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.
Proper citation: Information Artifact Ontology (RRID:SCR_000477) Copy
A searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. Two categories exist: Best Bets and Cutaneous Fields of Peripheral Nerves.
Proper citation: Neurosciences on the Internet (RRID:SCR_000478) Copy
https://github.com/GregoryFaust/samblaster
Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Proper citation: SAMBLASTER (RRID:SCR_000468) Copy
An open mark-up language for NMR data.
Proper citation: nmrML (RRID:SCR_000467) Copy
An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.
Proper citation: TAPyR (RRID:SCR_000588) Copy
http://open-ms.sourceforge.net/documentation/knime-integration/
A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.
Proper citation: TOPPAS (RRID:SCR_000533) Copy
The UK's professional body for chemical scientists, supporting and representing members and bringing together chemical scientists from all over the world. This not-for-profit organisation has an international publishing business and their activities span education, conferences, science policy and the promotion of chemistry to the public. They have offices in Europe, Asia, North America and South America.
Proper citation: Royal Society of Chemistry (RRID:SCR_000494) Copy
A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.
Proper citation: Oncotest (RRID:SCR_000489) Copy
http://carta.anthropogeny.org/
A virtual organization that promotes transdisciplinary research into anthropogeny, or the study of human origins. The research interests are broad and include finding the structural and molecular differences between humans and apes, identifying and explaining external mechanisms, and defining the evolutionary origins of humans. The center hosts symposia as well as visiting professors for the anthropogeny graduate program.
Proper citation: CARTA (RRID:SCR_000525) Copy
Established in 1985, The ALS Association is the only national non-profit organization fighting Lou Gehrig's Disease on every front. By leading the way in global research, providing assistance for people with ALS through a nationwide network of chapters, coordinating multidisciplinary care through certified clinical care centers, and fostering government partnerships, The Association builds hope and enhances quality of life while aggressively searching for new treatments and a cure. As the preeminent ALS organization, The Association leads the way in research, care services, public education, and public policy giving help and hope to those facing the disease. The Association's nationwide network of chapters provides comprehensive patient services and support to the ALS community. The mission of The ALS Association is to lead the fight to treat and cure ALS through global research and nationwide advocacy, while also empowering people with Lou Gehrig's Disease and their families to live fuller lives by providing them with compassionate care and support. The ALS Association has committed more than $58 million to find effective treatments and a cure for Lou Gehrig's Disease. Our global research effort has helped increase the number of scientists working on ALS, advanced new discoveries and treatments, and has shed light on the complex genetic and environmental factors involved in ALS. Diversity exemplifies The ALS Association's research philosophy. The Association spearheads investigator-initiated projects that originate from the minds of scientists. It also has ALS Association-initiated projects in which research ideas come from a small, blue ribbon committee of scientists who reach out with specific projects for designated scientists in the field. The ALS Association offers multi-year grants to established investigators, as well as one-year starter research awards. The Association is proud to administer The Milton Safenowitz Post-Doctoral Fellowship for ALS Research, which is the only post-doctoral fellowship for ALS research. In addition, The ALS Association's Sheila Essey Award, the premier ALS award, recognizes achievement in research. The ALS Association holds workshops each year that bring together scientists researching ALS and other neurodegenerative diseases to generate new research suggestions and fresh insight. In addition, our TREAT ALS (Transitional Research Advancing Therapy for ALS) initiative combines efficient new drug discovery with priorities set for existing drug candidates to accelerate clinical testing of compounds with promise for the disease. Our Clinical Management Research Program focuses on managing the care of people with ALS in such areas as nutrition, respiration, mobility and psychosocial needs. Since 1998, The Association has funded 21 clinical management research projects representing a total commitment of $750,000. The Association produces a series of manuals and videos as well as a DVD, called Living with ALS, that educate patients about all aspects of the disease.
Proper citation: ALS Association (RRID:SCR_000442) Copy
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