National Centers for Systems Biology
Searchable Database (All Resources)
The National Centers for Biomedical Computing (NCBC) has created a system called Biositemaps to allow scientists to share resources such as software, data, materials and services, as well as discover and utilize the resources published by others. National Centers of Systems Biology researchers are working with the NCBC to publish Center resources through Biositemaps. Below you can search and browse these resources.
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If you are looking for a particular type of resource, you can enter a search term here to search the Biositemaps database. You may focus your search on National Centers of Systems Biology resources, or you may broaden your search to include all research programs.
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Below is a table containing all National Centers of Systems Biology resources from the Biositemaps database, for those who would prefer to browse.
| Name | Description | Organization | Center | Contact | |
|---|---|---|---|---|---|
| Addama | “Data management – An adaptable data management system designed to support the mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). “ | Institute for Systems Biology | Center for Systems Biology | Ilya Shmulevich | |
| Adhesome | Literature-based protein-protein interaction network extracted from publications describing functional interaction in adhesion complexes of mammalian cells. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Advanced Imaging Core | The Centerâs Advanced Imaging Core (AIC) is currently employing a confocal imaging system coupled to a microfluidics platform to measure spatiotemporal expression of fluorescence tagged transcription factors in live embryos. The spatiotemporal expression of various transcription factors is currently investigated in the Center in different temperature regimes and mutational backgrounds using a precisely controlled microfluidics environment. One example of a microfluidics device developed by Center investigator Dr. Rustem Ismagilov is a dual laminar flow, which is used to supply two different temperature streams over a live Drosophila embryo within a microfluidic channel | Institute for Genomics and Systems Biology | Chicago Center for Systems Biology, Chicago, IL | Aharon Solomon | |
| Advanced-Correlation-Techniques-Group | Working group to discuss research advances and applications related to correlation techniques in advanced microscopy imaging tools. | University of California Irvine | Laboratory of Fluorescence Dynamics (LFD) | Michelle Digman | |
| Arabidopsis-Indel-Array | genotyping array built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). This array assesses 240 unique markers in a single hybridization experiment at a cost of less than $50 in materials per line. | Harvard FAS Center for Systems Biology | Center for Modular Biology | Christine Queitsch | |
| AVIS | The AVIS Viewer is a visualization tool for viewing and sharing intracellular signaling, gene regulation and protein interaction networks. AVIS is implemented as an AJAX enabled syndicated Google gadget. It allows any webpage to render an image from a text file representation of signaling, gene regulatory or protein interaction networks. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| BAC-Recombineering Core | BAC-Recombineering Core can provide investigators the capability to dynamically image fluorescently tagged proteins in model organisms and measure spatiotemporal expression of protein of interest. | Institute for Genomics and Systems Biology | Chicago Center for Systems Biology, Chicago, IL | Aharon Solomon | |
| Bayesian-Factor-Regression-Models | “Statistical software for modelling and analysis of sparse latent factor models, pathway analysis and predictive modelling with large-scale gene expression data sets.” | Duke University | Center for Systems Biology | Mike West | |
| Body-composition-and-bone-density-data | “Measurements of body weight, four different fat pad weights, bone mineral density and bone geometry were taken from SM x NZB and NZB x RF mouse intercross populations.” | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Cancer-Module-Map | “Web access to comprehensive modular analysis of transcriptional responses in human cancer, including the full cancer expression compendium, detailed clinical annotations, and all the significant modules. Various searching, browsing and visualization capabilities are provided.” | Harvard FAS Center for Systems Biology | Center for Modular Biology | Aviv Regev | |
| CellNetOptimizer | MATLAB toolbox for creating logic-based models of signal transduction networks, and training them agains high-throughput biochemical data | Harvard Medical School/ M.I.T. | Center for Cell Decision Processes, Boston, MA | Julio Saez-Rodriguez | |
| CGD-GBrowser | “GBrowse has been employed to connect datasets produced by Center for Genome Dynamics projects to locations within the mouse genome. In addition to the genomic location, information about the genes and single nucleotide polymorphisms that are present in the same area is also provided. Data currently displayed in the Centerâs GBrowse include imputed ancestry from the analysis of 12 strains of mice, along with the phylogenetic trees produced for those regions. “ | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| CGDSNP | “SNP Database â CGDSNP is a high quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources. “ | The Jackson Laboratory | Center for Genome Dynamics | Lucie Hutchins | |
| Computational Core | This Core relays on standard bioinformatics tools as well as specialized tools such as: * Cistrack: Cistrack is a repository for transcriptional network studies. * Flynet: Flynet provides an integrated view of Drosophila melanogaster transcription regulation and makes genome wide in vivo protein-DNA interactions data available to the scientific community as a whole. * The Chicago Utility for Biological Sciences (CUBioS): The CBC/CUBioS project is an open-source cloud-based bioinformatics platform. Cistrack is CUBioS instance. CUBioS is available from Source Forge and can be customized to support a variety of bioinformatics applications. | Institute for Genomics and Systems Biology | Chicago Center for Systems Biology, Chicago, IL | Aharon Solomon | |
| Cytoscape | Data Analysis – An open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. | Systems Biology community | Systems Biology Community at large/Center for Systems Biology | Ilya Shmulevich | |
| DataRail | Open source MATLAB toolbox for managing, transforming, visualizing, and modeling data, in particular the high-throughput data encountered in Systems Biology. | Harvard Medical School/ M.I.T. | Center for Cell Decision Processes, Boston, MA | Julio Saez-Rodriguez | |
| Differential-expression-in-C57BL-6J-chrYA | Chromosome Y (chrY) from the mouse strain C57BL/6J (ChrYC57) was substituted for that of A/J mice (ChrYA). Genome-wide gene expression was examined in cardiomyocytes from these mice. | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| DOQCS | A repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. | National Center for Biological Sciences (India), Bhalla Laboratory | Systems Biology Center New York | Upinder Bhalla | |
| Dynetica | “Gene circuit simulation software for graphical construction of kinetic models and automatic generation of the implied differential equations, time course simulations using deteriministic or stochastic algorithms, and sensitivity analyses.” | Duke University | Center for Systems Biology | Lingchong You | |
| Expression2Kinases | Software used to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| FNV | Written in Adobe ActionScript 3.0 the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Fungal-Orthogroup-Repository | provides the orthogroup assignments for all predicted protein-coding genes across 23 Ascomycete fungal genomes. | Harvard FAS Center for Systems Biology | Center for Modular Biology | Ilan Wapinski | |
| Gaggle | Database and software integration framework – The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data. | Institute for Systems Biology | Center for Systems Biology | Nitin Baliga | |
| GATE | GATE is a software system used to analyze time-series expression data. It creates cluster files from time-series data for visualization as movies. It used prior knowledge interaction networks and gene-lists libraries for identification of biological themes identified using the clustering analysis. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Gaussian-Graphical-Models | “Statistical software for Bayesian analysis and search of graphical/network structures in the framework of Gaussian graphical models, with links to applications in gene expression studies.” | Duke University | Center for Systems Biology | Mike West | |
| Gene-expression-response-to-diet | Gene expression was compared between mice from 12 inbred strains who were fed either a standard or atherogenic high-fat diet. | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Genes2Networks | Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Genes2WordCloud | Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Genome-Interval-Overlap-Calculator | “Genome Interval Overlap Calculator is a general purpose application for calculating the interval-by-interval overlap between two input files. One use of this application is to use the output from the Mouse Indentical by Decent tool to “”filter out”" regions of the genome that are identical between two strains. This could be applied to QTLs, gene lists etc.” | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Globals-for-Images | Software analysis tools for image files derived from multiple spectroscopic techniques. | University of California Irvine | Laboratory of Fluorescence Dynamics (LFD) | Julia K. Hall | |
| Graph-Explore | “Software for dynamically displaying, exploring and modifying large graphs and networks, with a range of visualisation and interactive analysis facilities.” | Duke University | Center for Systems Biology | Mike West | |
| High-Throughput Genome Analysis Core (HGAC) | The High-throughput Genome Analysis Core (HGAC) is a state-of-the-art facility providing resources and services for ultra-high-throughput sequencing and large-scale microarray processing. Operated by the Institute for Genomics and Systems Biology, the HGAC facility is available to University of Chicago and Argonne National Laboratory investigators and their collaborators | Institute for Genomics and Systems Biology | Chicago Center for Systems Biology, Chicago, IL | Aharon Solomon | |
| Imputed-Genotype-Resource | We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 74 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Indicator-Vectors | “The indicator vectors preserved DNA character information and provided quantitative measures of correlations among taxonomic groups. This method is scalable to the largest datasets envisioned in this field, provides a visually-intuitive display that captures relational affinities derived from sequence data across a diversity of life forms, and is potentially a useful complement to current tree-building techniques for studying evolutionary processes based on DNA data.” | Mount Sinai School of Medicine, Sirovich Laboratory | Systems Biology Center New York | Lawrence Sirovich | |
| iScMid | Literature-based protein-protein and gene-regulatory interactions extracted from publication describing interactions in mouse and human embryonic stem cells. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| KEA | Kinase enrichment analysis (KEA) is a web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. The system draws from several available kinase-substrate databases to compute kinase enrichment probability based on the distribution of kinase-substrate proportions in the background kinase-substrate database compared with kinases found to be associated with an input list of genes/proteins. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Laboratory-of-Fluorescence-Dynamics | “The Laboratory for Fluorescence Dynamics (LFD) is a national research resource center for biomedical fluorescence spectroscopy. The LFD’s main activities are i) Services and Resources for state-of-the-art fluorescence measurements, microscopy and spectroscopy, ii) Research and Development to design, test, and implement advances in the technology of hardware, software, and biomedical application, and iii) Training and Dissemination of knowledge relevant to fluorescence spectroscopic principles, instrumentation, and applications.” | University of California Irvine | Laboratory of Fluorescence Dynamics (LFD) | Enrico Gratton | |
| Lists2Networks | Lists2Networks is a web-based software system used to analyze lists of mammalian genes. It creates a similarity matrix for many uploaded lists and compares the resultant lists to libraries of gene-lists from different categories. Users can create networks of lists and expand lists with prior knowledge networks such as protein-protein interactions, co-expression or co-annotation networks. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Liver-expression-of-B6C3H-6T-and-C57BL-mice | “The B6.C3H-6T (6T) congenic mouse was created to study biology behind both the bone mineral density (BMD) and the serum IGF-1 quantitative trait loci (QTL) and to identify the gene(s) underlying these QTLs. Female 6T mice have lower BMD and lower serum IGF-1 levels at all ages measured. As the liver is the major source of serum IGF-1, we examined differential expression in the livers of fasted female B6 and 6T mice by microarray. “ | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Mapping-Mutations-in-Yeast | Software for using microarray data on DNA hybridization to detect single feature polymorphisms (SFP) and use them to map genetic traits in crosses between different strain backgrounds. | Harvard FAS Center for Systems Biology | Center for Modular Biology | “Ayellet Segre, Andrew Murray” | |
| Micro-Western Array Core (MWA) | The Micro-Western Array (MWA) Core is a technological initiative designed to provide a quantitative platform for studies of abundance and modification of pre-selected protein targets. | Institute for Genomics and Systems Biology | Chicago Center for Systems Biology, Chicago, IL | Aharon Solomon | |
| MOOSE | MOOSE is designed to handle large complex simulations especially in biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. It is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. | National Center for Biological Sciences (India), Bhalla Laboratory | Systems Biology Center New York | Upinder Bhalla | |
| Mouse-Diversity-Genotyping-Array | The Mouse Diversity Genotyping Array is the most advanced high-density mouse genotyping microarray available. The probe annotation files and the genotypes in the Training Set associated with the array are provided. | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Mouse-Map-Converter | “Mouse Map Converter is a simple web interface for converting mouse genome coordinates between MIT Markers, Base Pair Positions and Centimorgan Positions. The conversion process is based on the newly calculated mouse map described in Cox et al. 2009 Genetics.” | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Mouse-Strain-Comparison | Mouse Strain Comparison allows you to build strain comparison expressions which are evaluated against the selected strain genomes. This can be used to determine where strains are Identical By State or where strains with a high phenotype differ from strains with a low phenotype etc. | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Multiple-trait-measurements-in-43-inbred-mouse-strains | “A phenotypic survey was performed on males and females of 43 inbred strains for body composition (weight, fat, lean tissue mass and bone mineral density), plasma triglycerides, HDL and total cholesterol, glucose, insulin, and leptin levels while mice consumed a high fat, high cholesterol diet.” | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| National-Short-Course-on-Systems-Biology-of-Morphogenesis | “This open access national short course in systems biology focuses on the “”Systems Biology of Morphogenesis and Spatial Information Flow.”" The course will be held annually at UCI starting in January 2011.” | University of California Irvine | Center for Complex Biological Systems | Felix Grün | |
| NRC-1–Peptide-Atlas | “Data analysis software – A Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. “ | Institute for Systems Biology | NIH/DoE/NSF/NASA/Center for Systems Biology | Nitin Baliga | |
| p-values-in-small-microarray-experiments | “Microarray data typically have small numbers of observations per gene, which can result in low power for statistical tests. We investigated permutation based methods for estimating p-values.” | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| PathwayGenerator | Automatically generated pathways from receptors to effectors created using the neuronal signalome. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Peptide-Atlas | “Information Resource – Atlas for human, mouse, yeast peptides from large set of tandem mass spectrometry data. Results processed through Trans-Proteomic Pipleine” | Institute for Systems Biology | Center for Systems Biology | Eric Deutsch | |
| PPARgamma2-gene-expression | Gene expression was examined in murine marrow-derived U-33 cells which represent a clonal cell line spontaneously immortalized in the long term bone marrow culture conditions. | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Presynaptome | Literature-based protein-protein interactions extracted from low-throughput experimental studies reporting interactions in mammalian presynaptic nerve terminals. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| PRIORITY-Software | Software package for de novo motif discovery. Its goal is to incorporate informative position-based priors into a collapsed Gibbs sampling algorithm. | Duke University | Center for Systems Biology | Alex Hartemink | |
| ProbCD | “Data Analysis – An open source analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.” | Institute for Systems Biology | NIH/Center for Systems Biology | Ilya Shmulevich | |
| ProbTF | “Data Analysis – A flexible, probabilistic framework to predict TF binding from multiple data sources that differs from the standard hypothesis testing (scanning) methods in several ways.” | Institute for Systems Biology | Center for Systems Biology | Ilya Shmulevich | |
| PTMScout | Web application for viewing and analyzing data from mass spectrometry experiments and other datasets for post-translational protein modifications. The goal of PTMScout is to provide a useable interface for biologists to easily work with large datasets of post-translational measurements. | Harvard Medical School/ M.I.T. | Center for Cell Decision Processes, Boston, MA | Kristen Naegle | |
| QuantBio-Tools | QuantBio Tools is a framework that provides a pipeline for common data manipulation and analysis tasks. It pieces together several of the individual software resources developed as part of the Center for Quantitative Biology at Princeton. | Princeton University | Center for Quantitative Biology | Mark Schroeder | |
| SERV | SERV (Sequence-based Estimation of Repeat Variability) is a web-based algorithm that predicts tandem repeats and their variability for an entered sequence / genome. | Harvard FAS Center for Systems Biology | Center for Modular Biology | Kevin Verstrepen | |
| Sig2BioPAX | Sig2BioPAX is a comand-line Java program that can be used to convert structured text files describing molecular interactions into the BioPAX Level 3 standard format | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Simcluster | Data Analysis – Designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. | Institute for Systems Biology | NIH/NIAID/Center for Systems Biology | Ilya Shmulevich | |
| SNAVI | SNAVI (Signaling Networks Analysis and Visualization) is Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. | Mount Sinai School of Medicine, Ma’ayan Laboratory | Systems Biology Center New York | Avi Ma’ayan | |
| Stiff-Reaction-Diffusion-Solvers | Fast Numerical Algorithms for Stiff Reaction-Diffusion Equations. Provdies Matlab and C codes based on a novel and efficient algorithm for Reaction-Diffusion equations that model spatial dynamics of complex biological systems. The numerical method used in the code is designed for effective treatment of stiff reactions in spatial systems. | University of California Irvine | Center for Mathematical and Computational Biology | Qing Nie | |
| Systems-Biology-Seminar-Series | A monthly seminar series for CCBS-affiliated scientists with interests in Systems Biology. The seminars are a mix of local and outside speakers. | University of California Irvine | Center for Complex Biological Systems | Cely Dean | |
| Temporal-gene-expression-during-sleep | Changes in gene expression in the cerebral cortex and hypothalamus were assessed following different durations of sleep and periods of sleep deprivation | The Jackson Laboratory | Center for Genome Dynamics | Imogen Hurley | |
| Trans-Proteomic-Pipeline | “Data analysis software – a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios.” | Institute for Systems Biology | Seattle Proteome Center (expired)/Center for Systems Biology | Eric Deutsch | |
| u-track | MATLAB software package for high density multiple particle tracking. | Harvard Medical School | Center for Cell Decision Processes, Boston, MA | Khuloud Jaqaman |
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