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http://www.mgc.ac.cn/TrED/

TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes.

Proper citation: TrED (RRID:SCR_005869) Copy   

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http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

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http://www.zmmsoft.com

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed. * ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux * ZMM can be used via the command-line interface * ZMM can also be used at Windows via a graphical user interface

Proper citation: ZMM (RRID:SCR_005741) Copy   

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http://www.sociopatterns.org/

SocioPatterns is an interdisciplinary research collaboration that adopts data-driven methodology with the aim of uncovering fundamental patterns in social dynamics and coordinated human activity. To achieve its scientific goals, the SocioPatterns collaboration also contributes to the development of new technologies for collecting relevant data. In particular, the collaboration supports the development of the SocioPatterns sensing platform, which uses wireless wearable sensors to gather longitudinal data on human mobility and face-to-face proximity in real-world environments. The SocioPatterns team also works on developing tools and techniques to represent, analyze and visualize the collected data. We increasingly use digital media and computational devices in our daily activities, and leave behind a sizable amount of digital traces while doing so. The proliferation of mobile devices, and the incorporation of various sensing technologies in these devices, will further add to this growing trail of data. The possibility to mine and analyze these data, and the scale at which this can be done on contemporary computer systems, affords a novel, data-driven approach in the investigation of various aspects of human behavior. The following collection of datasets obtained through the SocioPatterns sensing platform are available: * Infectious SocioPatterns dynamic contact networks * Hypertext 2009 dynamic contact network * Primary school cumulative networks * Infectious SocioPatterns

Proper citation: SocioPatterns (RRID:SCR_005739) Copy   

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http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

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http://www.na-mic.org/Wiki/index.php/SoftwareInventory

A free open source software platform consisting of the 3D Slicer application software, a number of tools and toolkits such as VTK and ITK, and a software engineering methodology that enables multiplatform implementations. It also draws on other best practices from the community to support automatic testing for quality assurance. The NA-MIC kit uses a modular approach, where the individual components can be used by themselves or together. The NA-MIC kit is fully-compatible with local installation (behind institutional firewalls) and installation as an internet service. Significant effort has been invested to ensure compatibility with standard file formats and interoperability with a large number of external applications. Users of the NAMIC Kit will typically use a combination of its many modular components. * 3D Slicer is a general purpose application. Biomedical researchers will typically use this software tool to load, view, analyze, process and save image data. Slicer has been implemented to interoperate with many other tools, including XNAT, which is an open source image database. * Slicer modules, which are dynamically loaded by Slicer at run-time, can be used to extend Slicer''''s core functionality including defining graphical user interfaces. Modules are typically used by algorithms and application developers. * Application and algorithms developers may also use NA-MIC Kit toolkits and libraries. For example, the Insight Segmentation and Registration Toolkit ITK can be used to develop slicer modules for medical image analysis. The Visualization Toolkit can be used to process, visualize and graphically interact with data. KWWidgets is a 2D graphical user interface toolset that can be used to build applications. Teem is a library of general purpose command-line tools that are useful for processing data. Finally, those individuals wishing to create and manage complex software, the NAMIC-Kit software process is available as embodied in CMake, CTest, CPack, DART and the various documentation, bug tracking and communication tools.

Proper citation: NA-MIC Kit (RRID:SCR_005616) Copy   

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https://amu.edu.pl/

Research university in Poznań, Poland. It traces its origins to 1611, when under the Royal Charter granted by King Sigismund III Vasa, the Jesuit College became the first university in Poznań.

Proper citation: Adam Mickiewicz University in Poznan; Poznan; Poland (RRID:SCR_011084) Copy   

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http://www.univ-amu.fr/

University

Proper citation: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France (RRID:SCR_011087) Copy   

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https://www.amc.edu/

One of the nation''s oldest private medical schools, prides itself in offering intimate, collegial environment which fosters humane values and genuine learning.Institution was founded in 1839. College still maintains policy of limiting enrollment to small group of carefully selected students.Trains doctors, scientists and other healthcare professionals.

Proper citation: Albany Medical College; Albany; New York (RRID:SCR_011089) Copy   

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http://www.auburn.edu/

Public research and land grant university in Auburn, Alabama. It is one of the state's two public flagship universities.

Proper citation: Auburn University; Alabama; USA (RRID:SCR_011099) Copy   

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https://www.einsteinmed.edu/

Private medical school located in the Morris Park neighborhood of the Bronx in New York City. Einstein currently operates as an independent degree-granting institute under the Montefiore Medical Center. It was part of Yeshiva University until 2016.

Proper citation: Albert Einstein College of Medicine; New York; USA (RRID:SCR_011090) Copy   

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http://www.anthonynolan.org/Healthcare-professionals/Research-at-Anthony-Nolan.aspx

The Anthony Nolan Research Institute is fully dedicated to improving the outcome of bone marrow transplantation (BMT). The three main problems in BMT are graft versus host disease (GvHD) which is caused by differences in human leucocyte antigens (HLA), viral infection and the separation of GvHD from the graft versus leukaemia effect (GvL). Therefore, the five main aims of our Research Institute are the: # Investigation of the significance of HLA disparities between donor and patient at the molecular level and to analyze their influence on the outcome of bone marrow transplantation (BMT). # Maintenance and development of the HLA and KIR Sequence Databases. # Isolation and characterization of antigenic peptides from cytomegalovirus that act as targets for cytotoxic T-cell mediated responses. # Identification of target peptides and effector cells involved in graft versus leukemia (GvL). # Identification of target peptides and effector cells which initiate, maintain or perpetuate graft versus host disease (GvHD). During the past ten years our research team has made significant progress in many areas. For example, we have developed a new method that allows us to detect molecular differences that might be responsible for graft rejection and have identified CMV virus peptides that might be relevant in the future use of vaccinations. We are also studying the mechanisms of differentiation of the immune response after transplant and in this way we might be able to treat early stage GvHD. One of the most important activities of the Research Institute is orientated to academic teaching and training. We have established a structured research organization where a senior scientist is in charge of an individual research area and has under their supervision a team consisting of postdoctoral research fellows; PhD students and technicians. The teams interact with one another, as many of the projects overlap and this enables the sharing of experience and facilities.

Proper citation: Anthony Nolan Research Institute (RRID:SCR_011094) Copy   

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http://www.illumina.com/software/illumina_connect.ilmn

Software that estimates copy number and annotates regions with copy number variants(CNV).

Proper citation: CNVPartition (RRID:SCR_010925) Copy   

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http://www.stats.ox.ac.uk/~giannoul/GenoSNP/

A genotyping algorithm for the Illumina Infinium SNP genotyping assay.

Proper citation: GenoSNP (RRID:SCR_010928) Copy   

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https://launchpad.net/asterias

A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications.

Proper citation: Asterias (RRID:SCR_010936) Copy   

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http://chipster.csc.fi/

A user-friendly analysis software for high-throughput data.

Proper citation: Chipster (RRID:SCR_010939) Copy   

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https://www.uab.cat/

Autonomous University of Barcelona, is a public university mostly located in Cerdanyola del Vallès, near the city of Barcelona in Catalonia, Spain. As of 2012, the university consists of 57 departments in the experimental, life, social and human sciences, spread among 13 faculties/schools.

Proper citation: Autonomous University of Barcelona; Barcelona; Spain (RRID:SCR_011104) Copy   

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http://pfgrc.jcvi.org/index.php/bioinformatics/ginkgo.html

A spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ginkgo (RRID:SCR_010931) Copy   

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http://banneralz.org/

A leading destination for Alzheimer's disease care and treatment through research.

Proper citation: Banner Alzheimer's Institute; Arizona; USA (RRID:SCR_011107) Copy   

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http://www.bgsu.edu/

Public research university in Bowling Green, Ohio with nationally recognized programs and research facilities in the natural and social sciences, education, arts, business, health and wellness, humanities and applied technologies.

Proper citation: Bowling Green State University; Ohio; USA (RRID:SCR_011108) Copy   

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