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iCR / identify Conserved target of a Regulon
Permits high throughput, detailed and fully automated prediction of potential binding. iCR is a web server tool, for identification of conserved high priority targets of a regulatory protein from heterologous sequence data of prokaryotes (which includes regulatory sequences of genes and their orthologs in other species). Users can easily distinguish biologically important motifs from background noise based on their cross-species conservation.
Swinger
Automates breeding group selection for founding breeding programs. Swinger is a computer program designed to be highly flexible, with the user able to decide the number and sex composition of breeding groups and the allowable level of internal and pairwise relatedness given the available resources for captive breeding and the biology of the species. It has a user-friendly graphic interface and input parameters that are highly flexible to the reproductive system of the target system and the biotic and abiotic resources available for captive breeding.
AlphaMate
New
Optimizes selection, maintenance of genetic diversity, and mate allocation in breeding programs. AlphaMate’s goal is to find a valid mating plan that delivers desired targets. It enables both animal and plant breeding programs to be more optimal and aims to simplify new research opportunities. This tool can be applied in two cases: (1) maximizing efficiency of converting genetic diversity into genetic gain in a rapid recurrent genomic selection program for wheat; and (2) expanding the gain-diversity frontier with genome editing.
IMGui
Provides a graphical user interface (GUI) for the latest Isolation with Migration (IM) program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of runs, and visualizing results. It is developed using node. js and the Electron framework. IMGui can be used across operating systems and platforms, allows interactive validation and monitoring of runs, produces trace-plots and histograms of run parameters at regular intervals, and assists with mining run outputs to create publication quality graphs and visualizations.
FILET / Finding Introgressed Loci using Extra-Trees
Determines if a genomic window has experienced gene flow between two related populations and their direction. FILET proceeds by leveraging population genomic data from these populations. This software uses deep learning methods and works by combining information from several population genetic summary statistics that keep patterns of variation across these two populations. It assigns a genomic window according to three classes: introgression from population 1 into population 2, introgression from population 2 into population 1, and the absence of introgression.
SIPPOM-WOSR / Simulator for Integrated Pathogen Population Management adapted to study blackleg on Winter OilSeed Rape
Assesses and ranks Integrated Crop Management (ICM) strategies. SIPPOM-WOSR is a simulator for integrated pathogen population management. It is a model that links epidemiological, population and crop model approaches, simulating both quantitative (size) and qualitative evolution (genetic structure) of the L. maculans population. It is useful for designing and assessing cropping systems that seek to control phoma stem canker while both preserving the efficacy of specific resistance and meeting requirements of ICM.
Model for communicable disease outbreak dynamics
Provides a method for computing spread of infections. Model for communicable disease outbreak dynamics provides a repository composed of a simulator coupled to an Engine for Likelihood-free model. The application is based on the birth-death (BD) process which aims to improve the identifiability issues and estimation of the underlying infectious population size estimation. It was tested on epidemiological data collected about tuberculosis (TB) in the San Francisco Bay area.
GameChangingInnovations
Incorporates characteristics of human innovation and offers an explanation for one of the puzzling observations in the archaeological record of stone tools: its extreme punctuation. GameChangingInnovations encompasses two realistic ways in which innovations can affect the trajectory of cultural evolution: one in which a large-scale innovation, for example a more effective subsistence strategy, can alter the population size and thus the cultural steady state of the population, and one in which a large-scale innovation, such as writing or other mechanisms of preserving cultural information, can affect the rate of cultural loss. With all external factors remaining constant, a population’s cultural gains and losses reach an eventual cultural steady state, such that the rates of cultural innovation and loss balance one another and the population maintains a relatively stable number of tools.
THE REAL McCOIL
Estimates complexity of infection and population allele frequencies using single nucleotide polymorphism (SNP) data obtained from Sequenom or similar types of SNP assays. THE REAL McCOIL is a Markov chain Monte Carlo (MCMC) method that facilitates population genetic analysis when there are polygenomic infections, which are common in many malaria endemic areas. It provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings.
GBIF Integrated Publishing Toolkit
Provides functions to i) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and ii) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. DOIs and citations can be automatically generated for datasets in a standard format; a new DOI can be assigned to a dataset each time it undergoes scientifically significant changes and a version history is kept for each dataset, allowing researchers to easily track changes all previous versions. The guiding design principles of the IPT were to support how data publishers actually use their own databases, and to facilitate the public sharing of datasets with the fewest possible obstacles.
EPIMIC
A simple and versatile homemade tool, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory, including clinical samples, tests and diagnoses. EPIMIC was specifically designed to detect abnormal events as IDs are rarely predicted and modeled. An abnormal event corresponds to an increase above, or a decrease below threshold values calculated based on the mean of historical data plus or minus 2 standard deviations, respectively. EPIMIC proved to be efficient for real-time automated laboratory-based surveillance and alerting at our university hospital clinical microbiology laboratory-scale.
VCOM / Vector Control Optimization Model
Assists users in optimizing the impact of combinations of interventions for the control and elimination of malaria transmission. VCOM is a modeling framework that describes the population dynamics of mosquito vectors for prediction of the impact of combined vector control interventions. The software can be useful in selecting interventions for vector control trials and operational research, and in the design of trials themselves. Advanced options are available to alter the parameter values of the mosquito ecology and intervention models.
Pheasant Habitat Simulator
Provides a platform allowing users to interact with a species-habitat model for ring-necked pheasant (Phasianus colchicus) encompassing at a spatial scale to on-the-ground. Pheasant Habitat Simulator transposes a statistical model of pheasant-habitat relationships in Nebraska into visualizations. The program is available as both a web application and a standalone software which permits to accommodate a wide array of statistical models and conservation challenges.
FastEPRR / Fast Estimation of Population Recombination Rates
Assists in estimating population recombination rate based on intraspecific DNA polymorphism data. FastEPRR allows users to create genetic maps and to study recombination hotspots in the genomic era. It can be supported by computer clusters and is suitable for the analysis of population genomic data even when sample sizes are large. Moreover, it can handle the missing data often encountered in genomic scale population data sets.
AlphaSeqOpt
Uses haplotypes derived from existing phased marker array genotypes to identify which individuals should be sequenced. AlphaSeqOpt is a heuristic method for allocating low-coverage sequencing resources. This method is extended with an approach to filter out rare haplotypes. It has two main steps: (i) the initial set selection, where an initial set of individuals is selected by iteratively choosing the individuals that are the most complementary to the ones already in the set according to a score function and (ii) the set refinement, where the initial set of individuals is refined through several rounds of exchanges.
Genotype Fingerprints
Summarizes personal genotypes, yielding 'genotype fingerprints' that can be readily compared to estimate relatedness. Genotype Fingerprints is based on locality-sensitive hashing. It computes ‘fingerprints’ of genome-wide single nucleotide polymorphism (SNP) array genotypes as reported by directly to consumers (DTC) genetics companies. This tool can be useful to recognize genotypes from the same individual, from closely related individuals, or from a known population, and to cluster individuals into sub-populations de novo.
Genalice
New
Provides a toolkit dedicated to next generation sequencing (NGS) analysis. Genalice consists of: (i) Genalice Map, to produce mapped file that can be used as basis for further investigating; (ii) Genalice Germline, that deals with single sample variant calling; (iii) Genalice Population, which can be used for increasing the efficiency of variants calling or for preforming trio analysis; (iv) Genalice Somatic, for variants comparison between samples and (v) Genalice CNV, for the detection of copy number variation.
CMIF / Causal Model Inference Framework
Formalizes causal relationships between somatic genomic events, signaling pathway activity and immune activity in the tumor. CMIF infers directed interactions between signaling pathway activity and immune activity by anchoring the analysis on somatic genomic changes. The software was used to propose 11 novel genomic drivers of T cell phenotypes in the breast cancer tumor microenvironment. Analysis was focused on breast cancer, but the methodological framework can easily be applied to many other forms of the disease.
CGI / Cancer Genome Interpreter
Supports the identification of therapeutically actionable genomic alterations in tumors. CGI (i) identifies validated oncogenic alterations in a tumor, (ii) predicts the effect of the remaining alterations of uncertain significance, (iii) reports the known influence of these variants on drug response according to the level of clinical evidence supporting it and (iv) lists the interactions of existing chemical compounds with genes bearing driver alterations.
TREHS / Temporary Rivers Ecological and Hydrological Status
Recognizes hydrological regimes of temporary rivers. TREHS can assist users in the understanding of riverine ecosystems and contributes to their sound management. It permits users to operationally monitor, assess and classify the regime of temporary rivers. This tool calculates the degree of hydrological alteration with an expert scoring method from the differences between the metrics obtained for the reference regime and the actual one.
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ALFRED / ALlele FREquency Database
Contains several information about allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is designed to be a resource for research and for education in diverse areas related to human genetic diversity. This database focuses on allele frequencies in diverse anthropologically defined populations. It includes contents about allele frequencies of polymorphisms with an emphasis on those polymorphisms that have been studied in multiple populations.
NEMiD / North-East India Microbial database
Provides information about microbial diversity in North-East (NE) India. NEMiD aims to answer primary and integrative analysis questions frequently asked by microbiologists and biotechnologists. The database contains more than 200 entries of bacteria, fungi, and actinomycetes along with research articles on database-related data. Users can query different types of information including details of the organism, molecular data and publications. NEMiD can be used to understand the microbial diversity pattern of the megabiodiversity region and to assist in identification of microbes.
IthaMaps
Provides an epidemiology database of haemoglobinopathies. IthaMaps offers illustrating data on a dynamic global to regional map. It allows integration of additional types of information and more detailed data. This online resource content can be divided into three classes: (i) country-specific information on existing haemoglobinopathy-related healthcare policies, (ii) country-specific information on the status of major haemoglobinopathies and (iii) relative allele frequencies of specific globin gene mutations at the national and regional level.
BISMaL / Biological Information System for Marine Life
Gathers information about marine biodiversity information. BISMaL contains a wide range of data including brief description on taxonomy, photographs, distribution map, videos and references for each species. The database also allows users to explore two specific components: occurrence records, which gathers information about how organisms were observed and collected; and taxon metadata, which provides taxonomic groups information by using the Linnaean classification system.
SCLD / Stem Cell Lineage Database
Obsolete
Stores information for both human and mouse cell types and lineages. SCLD is a database that provides a user interface for the curation. It also permits to browse cell type gene expression profiles and cell lineage maps. This resource is publicly accessible, directly user editable, and hyperlinked to a series of source databases. It also provides graphical lineage maps, graphical ontology building, cell type expression data and a variety of other data essential to stem cell biologists.
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