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Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy
https://sciex.com/products/software/proteinpilot-software
Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.
Proper citation: ProteinPilot (RRID:SCR_024414) Copy
https://sparta.readthedocs.io/en/latest/
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Proper citation: sparta (RRID:SCR_024349) Copy
https://www.malvernpanalytical.com/en/products/product-range/omnisec/accessories/omnisec-software
Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL.
Proper citation: OMNISEC (RRID:SCR_024485) Copy
http://pbil.univ-lyon1.fr/software/phyldog/
Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.
Proper citation: PHYLDOG (RRID:SCR_024487) Copy
Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.
Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy
Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.
Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy
Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.
Proper citation: MADOKA (RRID:SCR_024522) Copy
http://www.nationalacademies.org/nrc/
Private, non-profit institution dedicated to utilizing knowledge in science, engineering, technology and health to improve government decision making and public policy as well as increase public education and understanding. The council collects, analyzes and shares information and knowledge through activities such as consensus studies, meetings and workshops, and program and research management.
Proper citation: National Research Council (RRID:SCR_000446) Copy
Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy.
Proper citation: Partnership for Interdisciplinary Studies of Coastal Oceans (RRID:SCR_024637) Copy
http://www.ncbi.nlm.nih.gov/gquery
Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems.
Proper citation: GQuery (RRID:SCR_001455) Copy
CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.
Proper citation: Center for the Neural Basis of Cognition (RRID:SCR_002301) Copy
A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.
Proper citation: DPARSF (RRID:SCR_002372) Copy
http://niftyrec.scienceontheweb.net/
Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities.
Proper citation: NiftyRec (RRID:SCR_002499) Copy
http://mutdb.org/mutpredsplice/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism.
Proper citation: MutPred Splice (RRID:SCR_000594) Copy
A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM.
Proper citation: Statistical non-Parametric Mapping (RRID:SCR_002092) Copy
Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease.
Proper citation: Tissue Engineering Resource Center (RRID:SCR_000103) Copy
http://www.nitrc.org/projects/wlfusion/
Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012).
Proper citation: Wavelet-based Image Fusion (RRID:SCR_002007) Copy
Netherlands Organization for Scientific Research (NWO) is a research institute and regional funding source in the Netherlands.
Proper citation: Netherlands Organization for Scientific Research (RRID:SCR_000988) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.
Proper citation: Project Halo (RRID:SCR_000136) Copy
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