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http://sourceforge.net/projects/ngs-toolbox/
A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.
Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy
http://sourceforge.net/projects/operasf/
A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.
Proper citation: Opera (RRID:SCR_000665) Copy
http://www.psb.ugent.be/esb/PiNGO/
A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: PiNGO (RRID:SCR_000692) Copy
Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.
Proper citation: RMAP (RRID:SCR_000695) Copy
https://github.com/iontorrent/TMAP
Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.
Proper citation: TMAP (RRID:SCR_000687) Copy
http://www.temple.edu/medicine/departments_centers/basic_science/neuroscience.htm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A department within the Temple University School of Medicine, which focuses on the education and research. This organization also hosts seminar series in neuroscience, sponsors annual lectures in neuroscience, and organizes bi-annual one-day workshops. This department has collaborative projects with researchers from the microbiology, immunology, pharmacology, radiology and the center for substance abuse research departments.
Proper citation: Temple University School of Medicine, Department of Neuroscience (RRID:SCR_000720) Copy
A department within the University of Miami which offers both undergraduate and postgraduate programs in neuroscience. The graduate program provides neuroscience research training in biological, behavioral, and physical sciences. This organization also conducts research through 55 active laboratories.
Proper citation: University of Miami, Department of Neuroscience (RRID:SCR_000723) Copy
https://projects.propublica.org/nonprofits/organizations/364298517
Non-profit charitable organization that benefits philanthropy, voluntarism and grantmaking foundations, focusing specifically on private independent foundations programs. (http://non-profit-organizations.findthebest.com/l/558154/Makray-Family-Foundation)
Proper citation: Makray Family Foundation (RRID:SCR_000916) Copy
A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes.
Proper citation: Frontier Scientific Chemical Supplier (RRID:SCR_000914) Copy
University in Scotland, UK that provides undergraduate and doctoral degree programs.
Proper citation: University of Dundee; Scotland; United Kingdom (RRID:SCR_000997) Copy
Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs.
Proper citation: Tufts University; Massachusetts; USA (RRID:SCR_000994) Copy
Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases.
Proper citation: Pasteur Institute of Lille; Lille; France (RRID:SCR_000990) Copy
http://www.ced.co.uk/pru.shtml?spk7wglu.htm
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology.
Proper citation: Spike2 Software (RRID:SCR_000903) Copy
The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community.
Proper citation: NIH Office of Research on Women's Health; Bethesda; Maryland (RRID:SCR_000986) Copy
http://www.ntu.edu.tw/english/
A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences.
Proper citation: National Taiwan University; Taipei; Taiwan (RRID:SCR_000983) Copy
A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry.
Proper citation: National University of Singapore; Singapore; Singapore (RRID:SCR_000984) Copy
A laboratory dedicated to advancing health care through utilizing computation and imaging to new areas of medicine.
Proper citation: BWH Surgical Planning Laboratory (RRID:SCR_000869) Copy
Commercial company that produces simple EEG measurement devices compatible with phones.Develops proprietary non invasive brain monitors and advanced machine learning algorithms to detect constellation of biomarkers of pathologies in asymptomatic individuals, such as people with neurodegeneration, adverse drug side effects or brain cancer, and to ascertain intent including individuals who cannot otherwise communicate.
Proper citation: NeuroVigil (RRID:SCR_000866) Copy
A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.
Proper citation: FileMaker (RRID:SCR_000783) Copy
A non-profit organization that supports the advance of healthy aging through biomedical research.
Proper citation: American Federation for Aging Research (RRID:SCR_000806) Copy
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