Allows users to generate alleles. GetCrosses selects one allele for each locus from each parent to generate the alleles of a new individual and simulates offspring genotypes from a single-nucleotide polymorphism (SNP) file for their use in relatedness analysis. This tool is useful for researchers wishing to realize simulations for different pedigree and estimate the relatedness values for all relationships within the artificial pedigree.
Selects blocks following a reproducible set of conditions. Gblocks is a program that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. It provides a web server that implements important features to make its use as simple as possible without losing the functionality that it is necessary in most of the cases.
Codon Optimization Tool
Allows users to detect codon. Codon Optimization Tool runs on with two types of entry: a sequence type related to DNA bases or a sequence type related to Amino Acids. This tool allows users to manually enter position parameters for easy optimization.
Allows the investigation of visualization methods in intuitive ways based on filtering. BioVis Explorer is a web application informing users about visualization techniques. This method assists users in studying biological data sets proposed in publications from top-tier journals and conferences within a time range from 2000 to 2016. It also proposes taxonomy of various aspects of the data and visualization methods.
Text Visualization Browser
Informs about text visualization techniques. Text Visualization Browser is a web application that can be used for getting an overview of the field, teaching purposes, and finding related work based on various categories defined in a survey taxonomy. It classifies about 30 text visualization methods with regard to data source, underlying text representation and processing method, temporal aspects, and supports user interactions.
Presents a list of visualization technique thumbnails organized in a grid. SentimentVis Browser is a web application allowing users to access to category statistics and a summary table with an overview of the complete categorization. It assists users in monitoring of public opinion in social media, literature analysis for digital humanities, or support for research of sentiment and stance in linguistics and natural language processing (NLP). Users can submit additional entries thanks to a form available from the top panel.
Quantifies the transcriptome of a given organism or cell. cjBitSeq allows production of transcriptomic data and can be used to reconstruct the transcriptome using de novo or guided assembly, or to estimate the abundance of known transcripts given a reference annotation. It allows to estimate the marginal posterior distribution of subsets of transcript.
Infers genes with differential transcript usage. BayesDRIMSeq is a count-based method proceeding to a transformation of the whole sequence of posterior probabilities with respect to the ordering of the magnitude change of relative expression between conditions. It estimates the Bayes Factor of a differential transcript usage (DTU) model against a null model using Laplace’s approximation.
REQUIEM / RElative QUantitation Inferred by Evaluating Mixtures
Allows users to work on relative quantitation. REQUIEM is a program that provides information about the quality of the data without employing replicates, standards, or assumptions regarding the presence or amounts of intrinsic standards. It supplies both unbiased fold-change ratios and statistics that reveal inconsistencies and non-linearities in the data that are difficult to detect.
GRAD / GRadient Adaptive Decomposition
Provides an accurate definition of the energy barriers and related borders. GRAD is a program using a noise-filtering procedure to smooth the energy landscape, reducing the roughness due to errors. It also determines the barriers and related border. It finds the separation between states by maximizing the timescales associated with metastable states.
BNER / Biomedical Named Entity Recognition
Allows users to recognize important biomedical entities (such as genes and proteins) from text. BNER is a recurrent neural network (RNN) framework allowing capture of morphological and orthographic information of words. It utilizes an attention model to encode character information of a word into its character-level representation. It combines character and word-level representations and then feed them into the long short-term memory recurrent neural network (LSTM-RNN) layer to model context information of each word.
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.
SuSPect / disease-SUsceptibility-based Single amino acid variant phenotype PrEdiCTion
Recognizes disease-associated single amino acid variants (SAVs). SuSPect combines sequence and structural features with several other characteristics including network information to train a support vector machine (SVM) method. It can discriminate between disease-associated and neutral SAVs, as opposed to predicting an effect on protein function. This tool is able to predict the phenotypic effects of a set of mutations in non-human proteins.
Attributes protein sequences to both de novo and orphan reactions. BridgIT employs the reaction fingerprints to compare enzymatic reactions. It introduces an additional level of specificity by capturing the critical information of the enzyme binding pocket into reaction fingerprints. This tool can quantify the similarity of reaction fingerprints thanks to the utilization of Tanimoto score.
Predicts RNA binding proteins (RBPs). Deep-RBPPred is based on a deep convolutional neural network (CNN) that uses an RBP predicting model. It can minimize final loss function which is consisted of cross-entropy between the label and probability score and L2 regularization loss of neurons. This tool was used to predict the RBPs in 30 whole reference proteomics, both reviewed and unreviewed.
Epigenomics in JBrowse
Allows visualization of specialized sequencing data in epigenomics. Epigenomics in JBrowse is a collection of plugins designed for JBrowe. It includes visualizing base modifications and small RNAs as well as stranded-coverage tracks and sequence motif density. This tool permits users to visualize the quantity of 4mC, 5mC, 5hmC, and 6mA at single base-pair resolution. It offers several filtering options including by sequence context and base modification.
gcapc / GC Aware Peak Caller
Accounts for GC-content bias separately for effects related to protein binding and differential non-specific binding. gcapc is based on a mixture model. It reduces false-positive peaks for any predefined bin and improves agreement across laboratories. This tool allows independent adjustments of the signal and background signals and thus circumvents the confounding challenge and can be incorporated into most current peak callers.
Checks the infinite sites assumption (ISA) in single-cell sequencing data. This method is based on real tumor data. It employs power of single-cell sequencing to learn high resolution pictures of tumor evolution and accounts for the noise in such data. This tool was validated with simulation studies and then examines a variety of single-cell sequencing data sets, uncovering widespread violations of the ISA in human cancers.
aFC / allelic Fold Change
Measures the cis-regulatory effect size. aFC is applicable to expression quantitative trait locus (eQTLs) discovered by standard eQTL calling methods. It captures the mechanistic regulation of haplotype expression in cis. This tool provides uniform estimates from both allelic expression and cis-eQTL data, and replication of cis-eQTLs using orthologous allele-specific expression (ASE) data from the same samples can complement classical replication with an independent sample.
Allows users to make estimation of the reliability of spike-in normalization in single-cell transcriptome studies. SpikeIns employs plate-based protocols to proceed. It can be used for routine normalization of scRNA-seq data. This tool can be used to quantify the variance of the added spike-in volume across cells. It appears to be reliable enough for routine use in scRNA-seq data analyses.
Allows researchers to measure the quality of their dynamic functional connectivity (DFC) methods. dfcbenchmarker is based on four simulation methods: (1) the sliding window (SW) method that uses a continuous subsection of the data; (2) the tapered sliding window (TSW) method that is similar to the SW adding a larger weight to the time points closer to the centre of the window; (3) the spatial distance (SD) that uses data points that have similar spatial profiles and (4) the Jackknife Correlation (JC) method.
OMGene / Optimise My Gene
Optimises the agreement between gene models for orthologous genes in multiple species in order to improve genome annotations. OMGene aims to find the most consistent set of representative gene models for a set of inputted genes. It returns the single best gene model for each gene. This tool is able to cross-align amino acid sequences to the genomic regions of the genes of interest to find conserved translatable features.
REMAP / the Remote Ecosystem Monitoring and Assessment Pipeline
Allows development of classified maps of land cover at Landsat spatial resolutions. REMAP is based on the geospatial data storage and analysis capacity of the Google Earth Engine. It aims to support the global effort to assess the status of all ecosystem types on earth. This tool can sort land cover according to user-supplied training data and a set of globally available remote sensing datasets as predictor variables.
PLDbench / Protein-Ligand Docking benchmarking
Allows evaluation of peptide-ligand docking poses. PLDbench is a web based tool that offers three modules: single, benchmark and compare. It allows users to submit docked pose and to choose the original crystal ligand out of 57 peptide-ligand complexes. This tool permits to perform benchmark analyses based on a set of docked poses imputed by users. It can calculate root-mean-square deviation (RMSD) between original ligand and predicted pose previously given.
Allows determination of cyclically symmetric homomultimers. SymmDock a priori limits its transformational search space only to symmetric transformations. It is based on a geometry docking algorithm. This tool is able to generate a candidate set of transformations by utilizing local feature matching. It products a web page allowing display of predicted solutions. The whole multimer is created for each solution.
Allows users to perform assembly tasks and to simplify developments without sacrificing speed for correctness. PTools is able to deal with both coarse-grained as well as atomic resolution representations of biomolecular structures. It can be used for docking searches and provides tools to load and manipulate structures. This tool can be useful for preparation, setup, running and analysis of docking minimizations.
MS-HBM / Multi-Session Hierarchical Bayesian Mode
Derives functional parcellations of the cerebral cortex within individual subjects. MS-HBM takes into account inter-subject and intra-subject functional connectivity variability. It was applied to three multi-session resting-state fMRI datasets from the Genomic Superstruct Project, Hangzhou Normal University of the Consortium for Reliability and Reproducibility, and the Human Connectome Project.
ICEPOP / Immune CEll POPulation
Estimates the relative immune cell response for each cell type. ICEPOP uses gene names and the associated expression values from microarray data of mouse and human organ or tissue samples to work. It calculates the relative response scores for each immune cell type defined by the reference matrix made from public gene expression databases. It can analyze non-purified bulky samples such as whole organs or biopsy tissue.
BNW / Bayesian Network Web Server
Provides a web-based tool for comprehensive Bayesian network modeling. BNW allows users to load a text file containing a dataset, identify the structure of the network that best explains the data, perform parameter learning of the network and use the network to make predictions. Its interface permits users to specify options that can aid in identifying robust network structures and limit structure searches to biologically meaningful networks.
Allows major histocompatibility complex (MHC) peptide binding prediction. MetaMHCpan predicts peptide binders of a variety of MHC alleles (through MetaMHCIpan and MetaMHCIIpan). This tool uses several single prediction methods to better select a few of promising peptides for biochemical experimental verification.
Allows prediction of interaction partners of human PDZ domains. modPDZpep is a web application providing an online interface for structural analysis of modeled PDZ peptide complexes. It uses statistical pair potentials for scoring of binding energy and can also identify novel PDZ mediated interactions in human protein-protein interaction (PPI) network.
Allows users to extract Protein Data Bank (PDB) information that bypasses the limitations associated with domain-based classifications. ConTemplate can suggest conformations for the query on the basis of its structural similarity to other proteins in the PDB, including proteins with low sequence similarity to the query. This tool can be applied on a genome-wide scale.
Supplies a method for Taenia solium control and transmission. cystiSim is a software allowing design of future program according to T. solium and its elimination as a public health problem. It contains environmental contamination, host immunity and parasite mutation.
Provides a continuous optimization approach to extract active modules from protein protein interaction (PPI) networks. ModuleExtraction is a method that tries to optimize the objective combining both topological and active properties of a module, which reflects the functional organization mechanism in a complex system. This application was also generalized to the multilayer dynamic PPI networks, using an aggregation of multiple single layers.
Provides an active module identification algorithm based on a memetic method. EAModules offers a direct strategy on a set of nodes to get connected subnetworks, thus avoid complicated graph divide operations. This algorithm is a simple genetic algorithm (GA) with basic binary encoding scheme without connectedness guarantee to search highly scored module in molecular networks. This method can be used in general heuristic optimization algorithms like simulated annealing and genetic algorithm.
Enables the systematic determination of protein targets linked to phenotypic screen readouts. DePick determines targets specifically linked to chemical phenotypic screens of mammalian organisms. It first identifies the compounds with specific activity on a screening assay and predicts their targets. Then, it determines the predicted targets that are statistically enriched in the set of specific compounds.
pCMF / probabilistic Count Matrix Factorization
Provides factor model, takes advantage of the Poisson Gamma representation, with the use of Gamma priors on the distribution of principal components. pCMF is a dimension reduction method that is dedicated to over-dispersed counts with dropouts, in high dimension. It is based on matrix factorization method and is specifically designed to analyse single-cell RNA-seq data. This tool is suitable for data visualization and clustering.
Quantifies local boundary characteristics of a closed geometric shape. LobeFinder is a highly useful convex hull-based program that identifies key features such as pavement cell lobes. This method operates on cell perimeter coordinates extracted from images of pavement cells and returns an array of useful cell shape data. It also includes a value for lobe number and a map of their positions. It creates a coordinate system to quantify local growth behaviors at the interface of two cells.
TSM / Trauma Severity Model
Provides a machine learning model for risk prediction. TSM is a user-friendly software application developed to provide researchers access to risk prediction models. This method improves over established risk prediction models in terms of the Akaike's information criterion (AIC) and receiver operating characteristic curve (ROC) statistics without sacrificing probabilistic calibration, which gives it prognostic value in trauma system evaluations.
TMPM-ICD9 / Trauma Mortality Prediction Model based on ICD9
Provides a ICD-9 injury model. TMPM-ICD9 is a probit regression model which includes the model-averaged regression coefficients (MARC) values for the 5 most severe injuries sustained by a patient as predictor variables. This model represents a significant improvement in existing injury scoring systems based on administrative data. It is based on universally available ICD-9-CM codes and could be used by virtually any hospital caring for trauma patients.
Provides a useful screening operation for identifying their membrane-based segments. TM Finder is an application that automates and implements the concept of dual threshold hydrophobicity and nonpolar phase helicity requirements to locate protein transmembrane (TM) segments from primary sequences alone. This program also has the power to distinguish essentially unequivocally between membrane and nonmembrane proteins.
MPEx / Membrane Protein Explorer
Provides a membrane protein explorer. MPEx provides an extendable framework for physical and biological hydropathy analyses and for b-barrel identification screening. It provides three analysis modes of operation that include (i) physical scale hydropathy analysis, (ii) translocon-scale hydropathy analysis and (iii) b-barrel analysis. It also offers two utility modes that include (i) Totalizer for estimating the binding free energies of peptides to phosphatidylcholine interfaces and (ii) Data-Buffer Overlay, which allows storage and graphical comparisons of different sliding-window plots.
Provides a Gaussian process latent variable model for pseudotemporal ordering. GPseudoRank is a fully Bayesian pseudotime method to sample from a posterior distribution of permutations rather than continuous pseudotimes, capturing uncertainty and even bi- and multi-modality of the orderings in terms of permutations. It also allows to make long distance moves in this space with a good acceptance rate.
Provides a high-throughput image processing platform. WorMachine enables automated calculation of many morphological and fluorescence features, and accessible machine learning techniques for higher-level features-based analysis, such as classification and phenotype scoring. It combines the capabilities of different programs into one software. The user-friendly interface was designed to suit investigators with no background in MATLAB, image processing, or machine learning, and requires no additional plugins.
Provides automated analysis of nematode size and shape. WormSizer is an open source software written as a plugin for ImageJ/Fiji. This application is designed to work with a standard stereomicroscope or any other source of brightfield images. It can detect multiple worms per image and it returns measurements of length, average width, width at the middle of the nematode, and volume in absolute units. It can also be extended and incorporated into existing tools.
Provides independent C++ implementations of the SUPERB algorithm for counting trees on a phylogenetic terrace. Terraphast offers independent C++ library facilitate integration of important phylogenetic post-processing step into popular phylogenetic inference tools that are predominantly written in C or C++. This resource yields exactly the same results that SUPERB algorithm.
Allows simulation of movements and reactions of molecules within and between cells. MCell permits simulation of specific instance of chemical signaling, diffusion, and reaction of discrete neurotransmitter molecules in synaptic spaces. It can be useful for Monte Carlo simulation of diffusion in a volume or on a surface. This tool employs a Model Description Language (MDL) to define simulation input conditions and user-requested output.
Allows construction of computational cell biology models. CellBlender’s outputs can be used with cell simulation biophysics engines and specially MCell. It allows users to: (1) define molecules and reactions, (2) create geometric objects, (3) define named surface regions on the objects and (4) assign properties to those regions. This tool permits drawing plots of said simulation, visualization of animation of the molecule trajectories.
PSESM / Pseudo Standard Error based Scan Method
Allows performing a complete search for significant single nucleotide polymorphism (SNP) main effects and SNP x SNP interactions. PSESM was implemented in order to give scan results rapidly despite no high-performance computing facilities. It can determine the first-stage significance thresholds for controlling the trade-off between computational cost and analytic power. This tool is useful for highly homozygous genomes.
Offers a computational model of the brain’s visual system. PyTorch is based on an unsupervised inference model that can learn representations from complex data. It can be employed to determine and decode cortical responses observed with functional magnetic resonance imaging (fMRI) during naturalistic movie stimuli. This tool also provides a control model to predict cortical responses with supervised information.
Offers a user-friendly environment to develop genetic software. Pydigree allows users to create and manipulate genetic data. It provides functions for the simulation of both pedigrees and population-based datasets by a forward-time strategy. The user can specify acceptable rates of genotyping errors and genotype missingness. This tool is based on a standard Hidden Markov model (HMM). It is able to perform kinship and inbreeding coefficient calculation, variance component estimation and forward time simulation of pedigree datasets.
SNP-IT / SNPs to Identify Tuberculosis
Recognizes all subspecies, lineages and sub-lineages for Mycobacterium tuberculosis complex (Mtbc) based on single nucleotide polymorphism (SNP). SNP-IT employs the entire library of lineage defining SNPs such that this is not an issue unless it occurs at the majority of lineage informative positions. This routine diagnostic workflow aims to improve understanding of the epidemiology and pathogenicity of the less common members of the Mtbc.
HiMAP / Highly Multiplexed Amplicon-based Phylogenomics
Produces phylogenomic datasets using highly multiplexed amplicon sequencing. HiMAP employs amplicon sequencing based on highly multiplexed polymerase chain reaction (PCR) to generate its datasets. It provides features for locus selection, primer design, target amplification, sequencing, and post-sequencing data processing and analysis. The method requires minimal hands-on time at the bench, and data can be processed rapidly for consensus calls that permits avoiding read mapping or assembly.
TNER / Tri-Nucleotide Error Reducer
Estimates the background from healthy subjects by creating samples. TNER is based on tri-nucleotide context data and employs a binomial distribution for the mutation error to proceed. It was evaluated on data from three healthy subjects that were not part of the background cohort. This tool allows users to improve the accuracy of mutation detection in circulating tumor DNA (ctDNA).
Permits normalization of 3C-like data. Binless is able to compute matrices that adapt to the size of the features present in the data. It aims to take genomic and polymer effects out of the data. This task is executed by a background model capturing local genomic effects and the calculation of a global distance decay. This tool allows normalization, interaction and difference detection entirely without specifying a Hi-C matrix resolution.
Produces fine level taxonomy classifications. TaxAss is based on an ecosystem-specific database and a comprehensive database to maintain the full biological diversity, taxonomic richness and accuracy of an amplicon dataset. It sorts operational taxonomic units (OTUs) that share high percent identity with ecosystem-specific reference sequences. This tool was applied on a variety of freshwater amplicon datasets and more specifically to the ecosystem-specific Freshwater Training Set (FreshTrain).
EditR / Edit Deconvolution by Inference of Traces in R
Measures base editing efficiency. EditR can produce a graphic of the percent noise across the sequencing file to assess the sequencing quality. It requires only a single Sanger sequencing file of a base edited sample and the sequence of the gRNA protospacer to disentangle the outcomes of base editing. This tool takes advantage of the proportional change in the percent area of trace fluorescence as bases are edited.
Identifies tumour organ of origin and histology using the patterns of somatic mutation identified by whole genome DNA sequencing. This tool is based on machine learning techniques and can be useful for a variety of fresh and fixed clinical specimens. It can assist users in characterisation of cytological specimens such as those obtained via needle aspiration. This application was created on the basis of a collection of uniformly processed cancer whole genomes assembled.
Manipulates Gene Finding Format (GFF) and Gene Transfer Format (GTF) files to extract data. gffutils is a python package that can build a database to infer the gene and transcript extents. It offers features to convert particular data file into the GTF standard file format. This tool is able to take into account parent attributes and hierarchical classification.
Concatenates FASTA alignments to one file in different format. catfasta2phyml is able to verify if all sequences in the file are aligned. It signals to users when an error is occurring.
Allows investigation of molecular interactions in cancer. Zodiac integrates big-data analysis on multimodal TCGA data and produces knowledge of molecular interactions in cancer. It is based on Bayesian graphical models. This tool contains a whole-genome and pair-wise interaction map, which offers intragenic and intergenic interactions of all pairs of genes in cancer. It is composed of the following features: data retrieval, computation, results assembly, and results dissemination.
Clusters sequences based on temporal dynamics rather than sequence identity. Ananke aims to group unique marker-gene sequences that are ‘‘dynamically similar’’. It complements traditional sequence-identity-based approaches such as operational taxonomic unit (OUT) clustering by examining the assumption that sequence similarity implies similar ecological properties. This tool employs time-series clustering and interactive data exploration.
Annotates expressed sequences tag (EST). EST-PAC is adapted for laboratories with limited bioinformatics resources and expertise. It offers a solution to implement a database system for the management of a complete suite of third party annotation software components, integrated into a simple and powerful web interface. This tool provides a workbench to cluster ESTs onto reference sequence data sets when available.
SSCC TD Simulator / Simultaneous and Serial Configural-cue Compound Stimuli Temporal Difference model simulator
Provides a model for representing compound stimulus configurations in a real-time architecture. SSCC TD Simulator is an extension of the Temporal Difference model which can be used for determining the hypothetic compound representation which can result from two or more stimuli that coexist according to specific conditions. It is also able to represent the formation of a compound representation of serial stimulus compounds.
Provides a R package introducing a statistical method for modeling disease transmission. The package allows users to settle individual-level spatiotemporal data, in a mechanistic manner or accounting for the general population. The software can be used to simulate epidemics among the general population and subsequently allowing a general epidemic predictive framework.
Bluetongue model for forward prediction of disease spread
Provides a method for study bluetongue transmission within and between sheep and cattle farms. Bluetongue model for forward prediction of disease spread is a flexible package which compiles data about on-farm transmission of bluetongue. It authorizes to gather multiple sets of simulated statistics on a same plot, for facilitating the comparison of simulations.
Allows users to perform image-based hemodynamics simulation. SimVascular is an open source software which provides a pipeline from model construction to simulation analysis. The software authorizes image processing, segmentation, meshing, as well as an interactive displaying of the results including point cloud visualization and volume rendering. It can be useful for cardiovascular basic science and clinical research and bioengineering education.
MIRT / Medical Image Registration Toolkit
Allows users to perform 2D and 3D non-rigid image registration. MIRT is a standalone software which includes six main features for completing: (i) similarity measures such as residual complexity (RC) or Correlation Coefficient (CC), (ii) transformation models both parametric and non-parametric, (iii) optimization, (iv) regularization, (v) a hierarchical registration and (vi) groupwise registration.
PDAC Disease Models / Pancreatic Ductal AdenoCarcinoma Disease Models
Provides a pipeline for analyzing whole-genome sequencing (WGS) data for simple somatic mutation (SSM), structural variation (SV) and copy number variation (CNV). PDAC Disease Models is a R package which provide a way for reproducing an experiment leads on Pancreatic Ductal Adenocarcinoma (PDAC) across ten primary-patient-derived xenografts (PDX) pairs, six metastasis-PDX pairs and five primary-PDX- patient-derived organoids (PDO) trios.
Allows users to handle rich phylogenetic data objects. Bio::Phylo is composed of over 50 modules which authorize several functionalities in manipulating and transforming objects such as annotation, sampling and simulations of tree topologies or visualization. It is designed to accept a wide range of inputs/outputs and also includes extensions packages which can be additionally downloaded.
Allows users to generate lists and trees of scientific names. Phylotastic is a web application which authorizes to users create lists from a URL, documents or from a specific taxon and to visualize the corresponding tree. Generated lists can be saved in a personal account and users can apply multiple options for managing, modifying and storing. The website also gives access to public lists which can be submitted by users.
PhyloWS / Phyloinformatics Web Services
Creates an interface for exposing phylogenetic data as web services. PhyloWS uses RESTful style web services and implements operations to relay data. The API generates a data structure, such as a tree, or a study, based on the queried phylogenetic information.
Provides a virtual portal that allows researchers to run multiple workflows. BioVel supplies a laboratory that gathers functionalities for supporting complex data biodiversity science and ecology research. It proposes workflow assortments in taxonomic refinement, ecological niche modeling, metagenomics, phylogenetics, population modeling, and ecosystem modeling which can be directly run or downloaded.
INFERNO / INFERring the molecular mechanisms of NOncoding genetic variants
Determines functional genetic variants underlying genetic association signals and characterizes their tissue-specific effects on regulatory elements, target genes, and downstream biological processes. INFERNO is a pipeline available both as: (i) a standalone software to perform the full process, and (ii) as a web application able to supply two default genome wide association studies (GWASs) datasets and to compute lighter analyzes.
GAPI / Geometric Analysis of the Protein Interactome
Provides a web tool for the geometric analysis of the human protein interaction network (hPIN). GAPI can compute hyperbolic distances between proteins, which hint at their likelihood of interaction. This application is based on a stringent subset of the Human Integrated Protein-Protein Interaction rEference (HIPPIE). It was embedded in the hyperbolic plane using LaBNE+HM. The resulting hPIN contains 10824 proteins with 66154 interactions (PPIs) between them.
Clusters protein databases by aggregating nearfull-length homologs. FastaHerder is an application that gathers sets of protein sequences and mines these clusters. This web app adds two clustering steps using a high threshold of sequence identity. This strategy allows, in addition, the ‘‘coclustering’’ of a query sequence to a preclustered database. FastaHerder is very restrictive in requiring the protein similarity to be full length.
CABRA / Cluster and Annotate Blast Results Algorithm
Provides a shortcut to the evaluation of a BLAST result where its clustering of hits allows a quick classification. CABRA integrates the advantages of a BLAST search and FastaHerder clustering algorithm into a single pipeline by annotating BLAST results clusters. Simplification and annotation of the results of a typical similarity search, as well as its ease of use and speed, provide an appropriate method of one-dimensional similarity search. The ability to set the identity threshold to group together query-like sequences is also an improvement over current clustering approaches.
RACCOON / Relative Amino aCid COmposition in dOmains and liNkers
Allows users to compare the mean amino acid composition of a specific domain to the mean amino acid composition of all domains, simultaneously for all available species. RACCOON is an application that provides combined analysis of domains and linkers. It provides interesting insights into their compositional differences and can give further pieces of evidence for models of molecular interactions. It could also potentially help with annotation of domains and linkers in new proteomes or be used to discover duplicated regions.
AMPtk / Amplicon ToolKit
Produces improved results of variable length amplicons from HTAS. AMPtk is a bioinformatic pipeline developed to specifically address the quality issues identified by using spike-in mock communities. It analyzes variable length amplicon studies such as the fungal ITS1 or ITS2 molecular barcodes. This method provides the scientific community with a necessary tool to study fungal community diversity.
Provides a free volume (3D image) viewer and segmentation tool. BrainSeg3D is a graphic application that make segmentation of volumes more accurate by providing tools for semi-automated segmentation combined with a user friendly graphic interface. This application is based on Seg3D, a free volume segmentation and processing tool. It was developed for medical professionals who need to perform image analysis as part of their research or for researchers working in the field of image analysis.
Evaluation of similarity measures
Provides a protocol that enables a thorough, optimization-independent, and systematic statistical evaluation of important similarity measure properties. Evaluation of similarity measures includes Accuracy (ACC), Distinctiveness of the Optimum (DO), Capture Range (CR), Number of Local Minima (NOM), Risk of Non-convergence (RON). The evaluation consists of three steps: (i) sampling of the parametrical space, (ii) computation of similarity measure values and (iii) computation of similarity measure properties.
TiDAL / Time-Dependent Activity Linker
Provides an integrative, time-centric method for antiviral network inference. TIDAL is a web application that creates a global view of the transcriptional network from a gene-expression time-series, identifies the transcriptions factors (TF) and relies them into a unified temporally-aware transcriptional cascade. It was applied to study data from influenza and measles.
Allows users to estimate Germinal Center (GC) volumes from standard multidimensional image data. pyBioImage is a cross-platform bioimaging application which supports several data formats and provides a way for visualization and analysis. The application includes a module: ExtractGC, based on a pseudo-recursive segmentation algorithm, which allows users to visualize the GC volumes in 3D while providing GC size and volume statistics.
Allows users to simulate the effect of peptide vaccination in cancer therapy. VaccImm provides a web platform allowing three kinds of analysis: prostate, kidney or a personalized simulation based on user-defined inputs. The application is able to model cancer immunotherapy based on cancer epitope sequences and major histocompatibility complex (MHC) genotypes. It includes a personal workspace for saving the simulations and an exchange forum.
GeVaDSs / Genetic Vaccine Decision Support system
Provides a platform for handle experimental results. GeVADSs is composed of modules that can be separated into two groups: (i) vaccine related modules, to process the biological data such as B-cell or t-cell module, and (ii) support modules, which manage data entry, report generation and data access such as quality control module. The application aims to improve development of novel vaccines by authorizing to analyze and compare data from different laboratories.
Offers visualization of the information relevant to selection of immunogen peptide sequences AbDesigner identifies optimal immunizing peptides for antibody production using a peptide-based strategy. It includes commonplace measures, such as conservation, hydropathy, possible modification sites, transmembrane domains. It also provides specialized display of 3D structural information from the Protein Data Bank (PDB), allowing users to view all information extracted from UniProt and PDB databases interactively.
OSCAR / Optimized Side-Chain Atomic eneRgy
Permits to models protein side-chain. OSCAR proposes several functions as (1) OSCAR-o for orientation-dependent energy functions and (2) OSCAR-d for distance-dependent energy functions. This tool was developed for the protein tertiary structure prediction using the high quality energy functions.
Allows users to compute multiple sequence alignments (MSA). MAFFTash is a web application that authorizes to perform sequences and structures through two software in a row. First, inputs are submitted to the ash tool: a structural alignment program which maximize the number of structurally equivalent residues between two proteins. Then, the structural alignment is analyzed by MAFFT to build the most consistent overall multiple alignment corresponding to it.
ASH / Alignment of Structural Homologs
Provides a structural alignment program. ASH, based on a double dynamic programming algorithm, intends to maximize the number of structurally equivalent residues between two proteins. The application includes functions for query and template PDB files as well as options for processing superposition and rotate structures. Moreover, the software provides tools for perform a faster alignment (RASH) or to align structures with multiple solutions (GASH).
REMOCOD / REgulatory MOtif COmbination Detector
Identifies pairs of transcription factor binding sites (TFBSs) in sequences of a set of co-regulated genes thanks to gene IDs. REMOCOD provides a web interface which detects over-represented TFBSs in the analyzed sequences and then, infers the corresponding regulatory motifs related to these. The software includes with an optional function permitting users to remove redundancy. It can be run only for men and mice’ genes.
SeSaw / Sequence-derived Structure Amignment Weights
Allows users to determine conserved sequence and structural motifs in proteins. SeSaw is a web application which provides a list of the templates accompanied by their corresponding annotated alignments and 3D structural superpositions, ranked by similarity. Users can choose to visualize all hits or only the representatives one. The software can be applied to structural genomics targets, homology models and immunology.
Allows users to identify peptide antigens and homologous peptide antigens. PAComplx is a web application which takes into account two T-cell receptors binding to peptide-major histocompatibility complexes (TCR–pMHC) interfaces from complete pathogen genome and experimental peptide databases. The application gives access to a wide range of information such as detailed atomic interactions, amino acid compositions of peptide families or source proteins.
Determines the conserved loci of rRNA genes’ orientation. V-REVCOMP is a standalone software, based on hidden Markov models (HMM), that is able to detect and reorient reverse complementary ribosomal sequences. Moreover, it highlights sequences with uncertain assignments or no detected HMM regions in any orientation. As well, it can also be used for detecting various sequence anomalies.
DynaMiteC / Dynamic Modeling and Clustering
Allows users to describe dynamics of the transcriptional response to a stimulus. DynaMiteC is a standalone software, based on a two-impulse model, which provides a method for generate time course gene-expression profiles while classifying them into clusters corresponding to different dynamical responses. The software was tested by detecting inflammation and anti-viral stimuli which can be find in mice primary dendritic cells.
Allows users to predict potential epitopes on protein. LocaPep is a standalone software, based on a new clusters algorithm, which allows prediction thanks to information provided by mapping peptides from a phage display library. The software provides a unique prediction that, by construction, is composed of close residues forming a single patch in the antigen surface.
ATIVS / Analysis Tools for Influenza virus surveillance
Provides a web application for generating antigenic maps. ATIVS can perform two types of analysis: a serological data analysis for all influenza subtypes and HA1 sequence data for influenza A/H3N2 viruses; and, a sequence data analysis to obtain predicted antigenic distances calculating until 500 sequences. It aims to help in observing antigenic evolution of influenza viruses and facilitate the selection of vaccine strains.
Manages data for high-throughput cytometry environments. WebFlow is an application, available from both a web application and a standalone software, which provides functionalities for: (i) data annotation, (ii) drawing gates and defining populations, (iii) exporting or visualizing data via heat maps and (iv) calculating standards and custom statistics. It aims to supply a unique platform to improve analysis and detection speed and accuracy.
Automates processing of intensity-based cell image segmentation. FLIM-FRET analyzer can separate objects of interest from the background to delineate whole cells. It simplifies image segmentation into single cells followed by donor lifetime and donor/acceptor fluorescence intensity quantification. For the software to work, users have to create a FRET collection which associates fluorescent intensity and fluorescence decay image datasets. To create a FRET collection, users import the donor and acceptor fluorescent channels and the donor fluorescence decay curves.
Allows identification of gene pairs associated with biological phenotype or clinical outcome. This program is an equivalent model subject to a sum-to-zero constraint on regression coefficients. It works jointly with an algorithm based on the alternating direction method of multipliers (ADMM). This association permits especially identification and model parameter estimation. This tool can cover compositional data and reference point insensitive data.
FLIMX / FLIM eXplorer
Allows the analysis of fluorescence lifetime imaging ophthalmoscopy (FLIO) data. FLIMX corrects the influence of the crystalline lens fluorescence on the approximated fluorescence lifetime of the retina. It implements known multi-exponential and stretched exponential approaches, as well as new layer-based multi-exponential approaches. It also grafts stochastic and deterministic minimization algorithms to determine the fluorescence lifetime parameters.