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http://sourceforge.net/projects/ldx/
A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.
Proper citation: LDx (RRID:SCR_012131) Copy
https://code.google.com/p/reditools/
A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.
Proper citation: REDItools (RRID:SCR_012133) Copy
http://pprospector.sourceforge.net/
A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.
Proper citation: PrimerProspector (RRID:SCR_012136) Copy
https://code.google.com/p/icelogo/
Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.
Proper citation: iceLogo (RRID:SCR_012137) Copy
http://musite.sourceforge.net/
A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.
Proper citation: Musite (RRID:SCR_012141) Copy
https://code.google.com/p/automotifserver/
Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.
Proper citation: AMS (RRID:SCR_012140) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
http://www.scienceexchange.com/facilities/pronovus-bioscience-llc
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024.
Proper citation: ProNovus Bioscience LLC (RRID:SCR_012266) Copy
https://code.google.com/p/hlaforest/
Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.
Proper citation: HLAforest (RRID:SCR_012146) Copy
https://www.promab.com/about-us
Develops and commercializes recombinant proteins and custom monoclonal antibodies through integration of bioinformatics, gene cloning, protein expression and purification, and immunology, using high-throughput technologies. ProMab applies its proteins and antibodies to deliver diagnostic products as well as services targeting the global biomedical market through collaborations with other biotechnology and bio-reagent companies.
Proper citation: ProMab Biotechnologies Inc. (RRID:SCR_012380) Copy
http://cran.r-project.org/web/packages/RJaCGH/index.html
Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
Proper citation: RJaCGH (RRID:SCR_008381) Copy
http://www.cerc.utexas.edu/OnlineCall/
A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.
Proper citation: OnlineCall (RRID:SCR_008263) Copy
http://www.bioinformatics.kmutt.ac.th/list-of-courses-2/
This program is an international Bioinformatics course at KMUTT designed for students who desire focused training in the elements of computer science, biology and biochemistry needed for a successful career in this exciting new discipline. Students in this program will receive comprehensive training in genomics, algorithms for sequence analysis, database design and management, software engineering and programming (including web-based development). Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia. In order to receive a Masters degree, students must demonstrate mastery of the core subject matter (expected to maintain a minimum grade of B in all core courses) and reach a minimum TOEFL test score of 500 (paper) or 173 (computer) or equivalent prior to or on completion of the course. In 24 monhs students gain the knowledge and skills necessary to enter a career with industry or a career in research as a bioinformatics or biocomputing specialist. The program offers fifteen scholarships each year include tuition and fees plus an additional to cover living expenses for 24 months. :Keywords: Bioinformatics, Computer Science, Biology, Biochemistry, Genomics, Algorithms, Sequence, Analysis, Database, Design, Management, Software, Engineering, Programing, Industry, Academia, Master''s, :
Proper citation: Bioinformatic: Programs and Courses (RRID:SCR_008379) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
Public research university in New South Wales, Australia which offers degree programs across a wide spectrum of disciplines, as well as providing research facilities to scientists
Proper citation: University of Wollongong; New South Wales; Australia (RRID:SCR_008322) Copy
http://www.agingintervention.org/
A 501(c)(3) non-profit organization that gives out grants created to develop new therapies to control and reverse the causes of aging, as well as treat and prevent the diseases of aging. The goal is to eventually control the processes of aging, reverse their effects, and stay younger longer and ultimately create indefinite youthful, happy and productive lifespan using innovative scientific methods that are under development today in biotech companies and research labs around the world. The foundation also offers education on what we can do now to stay younger, live longer and be happier while new therapies are being developed.
Proper citation: Aging Intervention Foundation (RRID:SCR_008288) Copy
http://www.strout.net/conical/
CONICAL is a C++ class library for building simulations common in computational neuroscience. Currently its focus is on compartmental modeling, with capabilities similar to GENESIS and NEURON. Future classes may support reaction-diffusion kinetics and more. A key feature of CONICAL is its cross-platform compatibility; it has been fully co-developed and tested under Unix, DOS, and Mac OS. Any C++ compiler which adheres to the emerging ANSI standard should be able to compile the CONICAL classes without modification. It is intended to encourage the rapid development of simulator software, especially on non-Unix systems where such software is sorely lacking. The present focus of the CONICAL library of C++ classes is compartmental modeling. A model neuron is built out of compartments, usually with a cylindrical shape. When small enough, these open-ended cylinders can approximate nearly any geometry, just as the stack of cylinders approximates a cone in the logo above. While any compartment has passive electrical properties (like a simple resistor-capacitor circuit), more interesting properties require the use of active ion channels whose conductance varies as a function of the time or membrane voltage. A standard Hodgkin-Huxley ion channel is included as one of the built-in CONICAL object types. Most of the voltage-gated ion channels in the literature can be directly implemented merely by setting the parameters of this class. For extensibility, this class is derived from several layers of more general classes. Connections between neurons can be implemented in several ways. For a gap junction (i.e., simple electrical connection), a passive current (or pair of currents, one in each direction) can be used. Synapses are more complex objects, but used in a similar fashion. The Alpha-function synapse is a very popular model of synaptic transmission, and is a basic CONICAL class. More complex (and realistic) synapses can be built using the Markov-model synapse. (A Markov model can be used on its own for other purposes as well.) In addition to classes directly related to neural modeling, CONICAL contains several other useful object types. These include a current injector, and a column-oriented output stream for storing data in table form.
Proper citation: Conical: The Computational Neuroscience Class Library (RRID:SCR_008318) Copy
http://www.med.nus.edu.sg/ant/histonet/txt/menu/nervmenu.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 18, 2013. 15 annotated electron micrographs of different parts of the nervous system. Different nerve tissues are depicted.
Proper citation: Nerve Tissue (RRID:SCR_008219) Copy
The mission of the Institute is to discover the key principles by which brains work and to implement these in artificial systems that interact intelligently with the real world. The Institute of Neuroinformatics is built of many people covering a wide range of disciplines and research areas. The major research projects and areas are listed below. - Behavior and Cognition: At the Institute of Neuroinformatics researchers investigate in Behavior and Cognition on various levels, ranging from neuronal circuit models of learning and adaptation over psychophysical experiments for color constancy up to modeling complex behavioral tasks such as exploration and goal-directed navigation. - Computation in Neural Circuits: By examining the brains of cats, rats and monkeys, and by making simulations of the cortex, INI hopes to learn how this circuit performs such widely different tasks. This knowledge might lead to advances in how computers are designed, and will certainly lead to advances in the subtlety and power of medical neuroscience. - Neurotechnologies: INI aims to harness the principles of biological computation, which can be expected to have a major impact on the technology market as autonomous intelligence pervades equipment, vehicles, buildings, utilities and clothing. Sponsors: INI is supported by European Union (EU), Gerbert Ruf Stiftung, Neuroscience Center (ZNZ), Swiss Confederation (KTI), Swiss Federal Institute of Technology Zurich (ETH), Swiss National Science Foundation (SNF), University of Zurich (UZH), and VW Stiftung
Proper citation: Institute of Neuroinformatics (RRID:SCR_008331) Copy
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