Precision Melt Analysis
Processes high resolution melt (HRM) analysis on genotype samples. Precision Melt Analysis is an application that permits users to characterize samples by considering sequence length, GC content as well as DNA sequence complementarity. It can be used for various analysis such as the scanning of new gene variants or the the determination of insertions or deletions. This program can be used with multiple real-time polymerase chain reaction (PCR) detection systems, including CFX Connect or CFX384.
Permits users to perform colorimetric and turbidimetric analyses, as well as report analysis for raw data, absorbance, limit, matrix, normalization, and curve fit. Microplate Manager is a program designed for reading the plate, generating an array of values, and performing data analysis. It supplies exact data with template design flexibility along with guides for designating plate wells, mapping dilutions, and multiple sample series.
Bio-Plex Data Pro
Assists researchers in observing multiplex data and understanding biological system. Bio-Plex Data Pro consists of a database application aiming to organize large volumes of multiplex data. This application is able to label samples with all biologically relevant information for data set comparisons. Additionally, this program offers the possibility to automate calculations with conservative statistics, select subgroups, and visualize results.
NASE / Nucleic Acid Search Engine
Offers a database search engine for RNA with a focus on high-resolution mass spectrometry (MS) data. NASE is an open-source software that reports oligonucleotide-spectrum matches with statistically meaningful false discovery rate (FDR) scores. It can support arbitrary modifications as well as salt adducts. This tool can also be downloaded as part of the OpenMS software.
AMBIORE / Applications for MCMC Bayesian Inference Of Rates in Evolution
Assesses rates in evolution starting from a sequence alignment and a tree topology relating the species. AMBIORE is a based on a model able to include context effects that are allowed to depend on sequence position and lineage. It aims to assist users in investigating complex models of the mutation and substitution process, and, extensively, to molecular evolution trends.
Proposes an assortment of statistical methods related to biosciences. BIOMStat provides features including: (i) basic analysis such as permutation tests, logistic and isotonic regression; (ii) approaches allowing the investigation of variance; (iii) sample and effect size estimator; (iv) modules for nonparametric and descriptive statistics encompassing Komolgorov-Smirnov test or Kendal’s rank correlation tau.
Enables matrix correlations for landmark data. Mace calculates significance of matrix correlations from permuting rows and columns of covariance matrices, maintaining the pairing of X,Y coordinates. This tool is able to perform significance tests including computation of repeatability, and bootstrap estimates of correlation statistics. It can transform covariance matrices into an "isotropic" version, in which all elements except for the diagonal are zero and all elements in diagonals are equal.
Aims to convert curves in semi-landmarks. SemiThinner allows saving of only semi-landmarks, landmarks only, or both landmarks and semi-landmarks. This application permits users to reduce the number of points to a specified number in all specimens.
Assists users with comparison via correlation analyses of matrices of distances among specimens or groups. Coriandis provides a set of analytical tools that aims to study associations among multivariate datasets such as shapes. It includes a graphical interface to determine which options users can apply for performing the analysis and which types of results can be produced.
Assists users in testing a priori models of morphological integration and modularity on multivariate data. Mint is an application that includes a module to carry out a variant of partial least squares (PLS) analysis on which a partition or putative module is regressed against the full set of traits. It also permits users to load individually created or edited models.
Assists users with the estimation and visualization of local deformations derived from landmark data. Lory is an application that uses shape information contained in landmarks to estimate, via interpolation, local deformations. It also provides a variety of useful visualizations (deformation grids, parrot plots, deformation movies), which can be exported at publication-quality resolution level.
Assists users in selecting bees for breeding. CBeeWing furnishes a solution for distinguishing bees of a more pure breed from other bees. This method was designed to permit researchers to find a queen in a colony of interest. Additionally, this tool can be used for analyzing CooRecorder bee wing files.
Consists of a chromatography data software (CDS) that allows chromatographic data samples to be executed. Empower furnishes solution assisting users in managing information, storage, and data mining capabilities. Additionally, it can be used jointly with other chromatographic techniques.
UNIFI Scientific Information System
Provides functionalities related to data acquisition, processing, visualization, and reporting. UNIFI Scientific Information System simplifies the management of quality control (QC) tasks, and the cooperation between different departments of a company. This program handles analytical tasks as a single, self-describing container that includes all of the results, the analysis method, and all of the audit trail history.
Automates liquid chromatography-mass spectrometry (LC-MS) data analysis routines. Symphony is a server application triggered by a MassLynx acquisition that allows the automation of data handling or processing functions in a sequence. It aims to reduce typical user errors when processing large datasets. This platform accepts several executables, batches and scripts.
Allows analysis and interpretation of all genomic variants from a single next-generation sequencing NGS assay. NxClinical is a program that gathers into one system cytogenetics and molecular genetics. The software permits consolidation of tests to provide copy number variation (CNV), absence of heterozygosity (AOH), and Seq Var from a single platform. It supports data from data from various manufacturers and technologies.
Performs 2-D gel analysis. Proteomweaver is a software solution that accelerates the process of protein analysis in the area of 2-D gel electrophoresis. The software contains leading-edge core algorithms for (i) spot identification, including the calculation of spot intensities, (ii) spot quantitation based on 3-D analysis, and (iii) spot matching, including the calculation of regulation factors. It is able to handle large amounts of experimental data.
Allows chimerism detection, quantification and analysis. ChimeRMarker was designed to integrate genotyping, analysis, and chimerism calculations by short tandem repeat (STR) polymerase chain reaction (PCR). The software can serve for monitoring chimerism level in both allogeneic stem cells transplant (SCT) or hematopoietic stem cells transplant (HSCT), bone marrow transplant (BMT), post bone marrow engraftment), and cord and peripheral blood stem cells transplant (PBSCT) samples.
Offers a platform dedicated to the analysis of single-source short tandem repeat (STR) data. GeneMarker HID is a program intending to assist users in project comparisons, encompassing the confrontation of edits and comments linked to the projects. This program can be used to custom STR multiplexes or, in forensic casework, as a tool for determining relationships such as paternity.
Intends to optimize a CE plate. GeneMarker MTP provides a four-steps workflow: (i) selection of a template including specialized ones, (ii) processing of the studied sample; (iii) reviewing of the size and allele calls and (iv) running of an application among more than 15 choices including relationship testing, tilling or haplotype analysis. This program can be used in conjunction with capillary electrophoresis platforms such as Beckman-Coulter.
Performs genotype analysis. GeneMarker is an application allowing the analysis of fragments. It includes a set of tools including a size template editor as well as a function to generate size calibration charts. It also provides features for analyzing multiplex ligation-dependent probe amplification (MLPA). This program can be used in conjunction with sequencing systems.
Proposes a platform for forensic mitochondrial DNA (mtDNA) analysis that uses a massively parallel sequencing (MPS) method. GeneMarker HTS allows (i) the browsing through the investigated data, (ii) the alignment of the homopolymeric sequences, single nucleotide polymorphisms (SNPs) and INDELs, (iii) the identification of phylogenetically correct primary haplotypes or heteroplasmic variants, (iv) the generation of reports and (v) the exploitation of the results for database searching.
MaSTR / Mixture analysis from STRs
Provides an approach to probabilistic mixture analysis. MaSTR utilizes user’s forensic acumen in a graphical environment for research, validation and casework applications. It provides flexible technology that allows custom modeling and development. This method includes two simultaneous user licenses, and automatic queuing of multiple analyses. This software does not need to be updated to include improvements to the statistical analysis as the science progresses.
Exploits Nature Genetics’ publications to perform genome-wide association studies (GWAS). Exemplar Analytics provides a set of discovery tools allowing: (i) analysis of admixture corrections copy number variation (CNV), quantitative traits and haplotypes; (ii) mapping of single nucleotides polymorphisms (SNPs) to their related genes; (iii) highlighting of multi-locus models, as well as (iv) a viewer able to display whole-genome, which handles layers from 10 to 500k array results.
MicroSEQ ID / MicroSEQ ID Microbial identification
Enables microbial identification. MicroSEQ ID is a component of the ‘MicroSEQ Rapid Microbial Identification System with Applied Biosystem’. This program allows the identification and the classification of unidentified bacterial or fungal sequences. It can assist users in streamlining workflows as well as implementing and following standard operating procedures.
NCG / Next-Generation Confirmation
Consists of a CE Sanger sequencing software hosted on the Thermo Fisher Cloud environment. NGC confirms variant identification by comparing trace files to a variants file generated on a next‑generation sequencing (NGS) instrument. The software performs single nucleotide polymorphism (SNP) detection and analysis, SNP discovery and validation, and sequence confirmation. It also retrieves reference sequences from genomic databases, reports variants in genomic coordinates, reports genomic annotations for SNPs, and generates a Venn diagram.
VA / Variant Analysis
Performs reference-based re-sequencing analyses such as single nucleotide polymorphism (SNP) detection and analysis, SNP discovery and validation, and sequence confirmation. Variant Analysis is a Sanger sequencing software hosted on the Thermo Fisher Cloud environment. The software analyzes trace files generated on ‘Applied Biosystems Genetic Analyzers’ to identify variants. It can automatically retrieve reference sequence from genomic databases, report variants in genomic coordinates, and report genomic annotations for SNPs.
Consists of a downstream analysis and interpretation software. DeepCheck handles sequencing data and can serve for performing genomic data analyses, such as genotyping, subtyping, amino-acid mutations detection, nucleotide changes characterization, as well as clinical interpretations.This program is available for different applications such as HIV or HBV, and is compatible with electrophoresis capillary and next generation sequencing (NGS) platforms. It can be used through a cloud access or locally, through pre-configured servers.
Offers a platform for downstream analysis. Viroscore provides a pipeline that manages the input data through a unified repository, perform analysis of interest, for instance amino-acid mutations detection, and lastly produces the corresponding reports. This program aims at being incorporated into networks related to user’s structure. It can be used for both genomic data analyses and for clinical interpretations.
Offers a platform dedicated to investigation related to methicillin-resistant Staphylococcus aureus bacteria (MRSA). StaphType is a program intending to assist users in typing MRSA by identifying and gathering information linked with their spa repeats and spa-types. It includes a repeat motif search, a report generator and a feature to locally host information from previous analysis.
Investigates data derived from a QuantStudio™ Digital PCR Kit on the QuantStudio™ 12K Flex instrument. DigitalSuite includes a set of function allowing: (i) import of data into experimental studies; (ii) definition of experimental plate setup; (iii) visualization of plate heatmaps, bar graphs, and cluster plots; (iv) target quantification; (v) data quality control (QC) applications; and (vi) features for exporting data for further downstream analysis.
Allows users to process and analyze quantitative polymerase chain reaction (qPCR) data. GenEX is an application that consists of two main parts: (i) the first part prepares data for statistical analysis and includes more than 10 operations such as interpolate calibration and normalization steps; (ii) the second part comprises a set of analysis encompassing the fields of cluster analysis, computation of correlation, generation of networks, regression analysis, and more.
HRM / High Resolution Melt
Detects variations in nucleic acid sequences. HRM is an application that can be run either locally or from the Thermo Fisher Cloud, with possible inter-operability among its two versions. It proposes a method that investigates polymerase chain reaction (PCR) melting curves to highlight the differences. The cloud application allows the simultaneous analysis of several plates whereas the desktop version offers an access to an additional set of data review tools.
Proposes a platform dedicated to analyzes in food pathogen detection. RapidFinder Express is an application intending to assist users in determining the absence or presence of pathogens in an area of interest. It includes functions which aim to optimize the thermal cycling conditions as well as an automatic feature to identify an optimal location for samples and controls.
FRAGAL / FRAGmented ALignment
Assists users with the pairwise alignment of sequences. FRAGAL is a fragmented technique that splits sequences into fragments of several amino acids, with the starting indices sliding across the sequence length in steps of multiple amino acids. The results can be filtered on the basis of an annotation file, allowing the corresponding segments to be manually inspected and annotated in a sequence of query proteins.
Optimizes the analysis of real-time polymerase chain reaction (PCR) amplification curves. RapidMAX leans on a control-based threshold (CBT) algorithm that investigates fluorescence of the positive controls. It proposes an automatic workflow intending to decrease the time consumed by this kind of analysis as well as to reduce human error and bias. This program is compatible with instruments such as Applied Biosystems 7500 and 7500 Fast.
Sequence Detection System
Provides high-throughput gene expression and genotyping analysis software. Sequence Detection System is an application that creates and saves analysis templates on a per detector basis for use with other plates. It can export the results or data, up to 50 plates at once, as well as a selection of results columns, using the batch export utility. This software was developed for use with the Applied Biosystems 7900HT Fast Real Time PCR System.
Attune NxT Software
Enables user-defined experimental analysis via a graphical interface. Attune NxT Software permits to adjust flow rates, compensation and voltages. It can also automate maintenance and instrument performance monitoring. It simplifies data acquisition with a dashboard that provides viewing acquisition status and setting acquisition stopping criteria. This application is used to operate and maintain the Attune NxT acoustic focusing cytometer.
Identifies areas for microdissection based on user-defined criteria. AutoScanXT is an optional image analysis program that automates identification of cells to, subsequently, reduce the overall time required to perform a microdissection experiment. It performs high contrast samples and can be used with colorimetric, fluorescence and immunohistochemistry (IHC) stained specimens. This software was developed for using with the ArcturusXT™ Laser Capture Microdissection (LCM) System.
Provides a suite of features for image analysis and visualization. Celleste proposes a workflow of tools including several capabilities for segmentation, classification, and quantification of single images or a batch of images. This application can be associated with the EVOS microscopes, allowing users to capture, save, process, measure, and analyze images and create data.
HCS Studio / High Content Screening Studio
Allows access to instrument configuration and control functions with software-resident protocols. HCS Studio provides visual feedback to enable custom assay protocol setup, image acquisition, analysis, and data visualization. This application works with Thermo Scientific Store Image and Database Management Software to analyze and store the resulting high content images and data.
Allows regulated laboratories to submit documents, including those with electronic signatures, to the Food and Drug Administration (FDA) in electronic form. LCQUAN permits to acquire and manage quantitative liquid chromatography-mass spectrometry (LC-MS) data. It performs method development, data review, processing, reporting, and data export. It also permits to import sequence information from other systems.
Assists users in screening, detecting, and characterizing intact proteins. BioPharma Finder is designed to verify and detect amino acid sequence and known/unknown post-translational modifications (PTMs) of relative amounts using a peptide mapping workflow. It also can serve for confirming different sequences along with identification and localization of modifications by using an automated top down workflow.
Consists of a suite of tools assisting researchers to find new science contents. Cortellis gives access to a range of data across the drug and device innovation lifecycle. The tools cover a large range of topics: drug pipeline, clinical trials, patents, deals, company and conference data. Additionally, this program offers a cloud solution including next generation analysis, visualization and workflow tools.
Assists users with clinical and diagnostic research. novoClinic is a patient-centric next generation sequencing (NGS) target sequence analysis application. It provides integrated sample tracking for quality control and compliance.
Permits users to design oligos for multiplex assays, facilitating amplification of multiple targets in a single reaction vessel. PrimerPlex is an application that designs optimal multiplex primer sets under uniform reaction conditions, for over 100 sequences. To ensure the specificity of the primers, they can be searched in BLAST from any of the genomic databases available at the NCBI.
Designs primers for loop-mediated isothermal amplification (LAMP) assays. LAMP Designer is an application that permits the amplification of DNA and RNA sequences at isothermal conditions. This software automatically interprets BLAST search results and allows the design of primers that have significant cross homologies with a local database. Multiple projects can be created, and data of multiple experiments can be managed by creating a separate project for each experiment.
Provides a primer designing software specifically developed for loop-mediated Isothermal amplification (LAMP), a gene amplification method. PrimerExplorer has several features: (i) it can design 4 primers based on 6 regions required by the LAMP method, (ii) it can design loop primers, and (iii) it uses the nearest neighbor method for Tm calculation.
Key Pathway Advisor
Assists users with biological pathway analysis of omics data. Key Pathway Advisor is a web application that predicts key protein activity changes. It permits the creation of hypotheses about new targets, mechanisms of action, biomarkers and disease associations. Users can align results with knowledge of putative biomarkers and drug targets.
Alissa Clinical Informatics Platform
Performs next-generation sequencing (NGS) and comparative genomic hybridization (CGH) data analysis, variant assessment and provides reporting modules designed to optimize workflows across technologies and applications. Alissa Clinical Informatics Platform includes (1) a variant assessment and reporting module, which builds variant assessments for both inherited disease and somatic assays and evaluates molecular and structural variants, and (2) a data analysis module for raw NGS data, which enables scalable alignment to called variants for detection, annotation, and visualization.
Provides an image analysis platform for quantitative tissue analysis in digital pathology. HALO includes modules that can be combined to improve the analysis workflow. It includes tools to assist users in automating tissue segmentation such as a tissue classifier, a serial section analysis module and a tissue micro array (TMA) segmentation add-on. It also provides a function to improve image processing speeds for high-throughput labs.
Offers flexibility and spectral visualization for Agilent’s FTIR spectrometers. MicroLab Expert is a program designed for use when spectral visualization and data processing are needed to reach the results. The software allows visualization of spectral information before and during collection. It also permits identification of spectra using functional groups, performing of basic kinetics analysis, and manipulation/processing of data using mathematical functions and algorithms.
Agilent Clarity Software
Aims to facilitate complex data interrogation and reporting. Agilent Clarity Software is a visualization program allowing compound identification and spectral analysis, including mathematical functions, such as variance, addition, averaging, and spectrum transformations. The software enables users to combine high spatial resolution compositional analysis with spectral library matching.
Provides an automated solution for micro-computed tomography (microCT) analysis and visualization. AccuCT permits researchers to perform american society for bone and mineral research (ASBMR) bone morphometry and bone mineral density (BMD) analysis. This imaging software was developed to work with data acquired on Quantum FX and GX microCT system. It also allows the export of images in high resolution for publications and presentations.
Assists users in predicting complexes of macromolecular structures. QUASI-RNP consists of a medium-resolution knowledge-based potential that aims to identify near-native protein-RNA complex structures. This solution is able to deal with RNA structures with post-transcriptionally modified residues. This tool has demonstrated its ability to select rigid body mooring positions during testing.
BSDD / Biomolecules Segment Display Device
Enables users to search and visualize a user-defined motif or fragment among the protein structures available in the Protein Data Bank (PDB). BSDD offers three functionalities for users queries: (i) ‘explore’ permitting researchers to see the header information or the complete content of the PDB file., (ii) ‘search using’, and (iii) ‘sequence matching’.
VSWarehouse / VarSeq Warehouse
Consists of a scalable, multi-project warehouse for next-generation sequencing (NGS) variant call sets, clinical reports and catalogs of variant assessments. VSWarehouse is built on the algorithms and storage technology powering the VarSeq software, allowing organization of samples in several fully-versioned projects. The software allows users to complete customizable report templates, which can be queried at the variant or at the sample level, and creates a single annotated matrix of all unique variants for all uploaded samples. It also hosts variant assessment catalogs.
VSClinical / VarSeq Clinical
Enables clinical interpretation of variants based on American College of Medical Genetics and Genomics (ACMG) guidelines. VSClinical implements a guided workflow for following the ACMG scoring and classifying guidelines. The software can gather conceptually related criteria and formulate them as answerable questions. It can provide recommendations for questions having bioinformatic evidences. This program also includes documentation and best practice excerpts.
Allows the analysis of images acquired on IN Cell Analyzer systems. IN Carta is an application based on algorithms that produces segmentation without requiring complex pre- or post-processing steps. This program includes functions permitting researchers to investigate image data, to generate image analysis protocols, and visualize analysis results, with included assistance all along the processes.
VS-CNV / VarSeq Copy Number Variant
Allows detection of copy number variants (CNVs) in next-generation sequening (NGS) data sets. VS-CNV uses changes in coverage relative to a collection of reference samples as evidence of CNV events. The software calls CNVs in target regions and avoid the cost and turn-around time of additional chromosomal microarray (CMA) or Multiplex Ligation-dependent Probe Amplification (MLPA) testing.
VSPipeline / VarSeq Pipeline
Enables repetition of clinical workflows, creation of high throughput pipelines and provides access to curated annotation sources. VSPipeline permits users to create workflow-encoded project templates which lock down quality control and filtering parameters. The software can also be used to generate deliverables such as annotated text or VCF files as well as multi-tab Excel reports of filtered variants, sample and coverage regions statistics.
VSReports / VarSeq Reports
Allows users to convert the output of their tertiary analysis into a customized clinical report. VSReports enables the selection of variants to be included in this report. It can be composed of identifiers from dbSNP or COSMIC catalogs, descriptions of gene function from OMIM, pathogenicity based on users past variant assessments or Clinvar, HGVS variant names, exon numbers, sequence ontology, coverage information, variant interpretations provided by the user and overall test interpretation.
Allows the control and supervision of chromatography systems as well as the evaluation and analysis of the results from separation runs. UNICORN is a four-steps approach which assist users in generating, editing or converting a method with different system types. Then, the software runs the created method, assesses its efficiency and compiles the results in a final report. It can be used for the evaluation of a column performance test.
Imaris for Cell Biologists
Offers a platform dedicated to the investigation of cells and organisms. Imaris Cell Biologists is a package consisting of five main parts: (i) a detection part with feature for membrane labelling or to identify nucleoli and protein clusters; (ii) a cell tracking part; (iii) a statistical module allowing to get information about motion analysis, cells, spots and surfaces; (iv) a comparison tool to confront multiple experimental groups and (v) a export managing feature for static images and animation.
Imaris for Neuroscientists
Proposes a toolkit for analysis in neuroscience. Imaris for Neuroscientists focuses mainly on detecting cells and structures and tracing neurons. It also includes various features from the Imaris software such as function for comparison and tracking algorithms. This program allows the visualization of multiple images (either in 2D, 3D or 4D) with differing spatial/temporal dimensions and resolutions.
Offers a platform to perform multi-step purification process. AKTAxpress is an application made for using in experiments implying antibodies and affinity-tagged proteins. It includes preoptimized purification protocols but can also be run in conjunction with the UNICORN software to assist users in generating a purification protocol. It can control more than 10 systems in parallel and, broadly, intends the decrease time-consuming tasks.
Investigates 3D and time-lapse microscopic images. Imaris Start is an application, composed of several modules from the Imaris software, that can be used for detecting cell and organelles, generating animations, quantitative information, comparison between multiple images as well as for leading co-localization studies, plotting and statistical analysis. It has been developed to analyze large datasets.
Allows the monitoring of automated liquid chromatography systems from the AKTAprime software. PrimeView consists of two main modules: (i) PrimeView System Control, that permits users to control separation processes; and (ii) PrimeView Evaluation, that assesses and reports results from separation processes. Additionally, the program provides a search function to locate items such as curves or chromatograms.
Imaris Single Full
Offers a platform to investigate image data. Imaris Single Full is a package of functionalities compiled from the Imaris software. It includes several features for: (i) identifying cells, membranes and surface; (ii) tracing neurons; (iii) measuring distances and (iv) generates various statistics dealing with spines, cells, filaments, dendrites, spots, surfaces, cell cycle and motion analysis; (v) and exporting image and videos for further publications.
Performs an automated alignment of overlapping 2D or 3D image tiles. Imaris Stitcher is an application that aligns and fuses microscopy image tiles into one 2D, 3D or 4D volume. It includes a function that is able to detect stage coordinates for every submitted tile and allows the alignment leaning on image content as well as in XYZ and can support large size images.
Assists users in forecasting toxicity. ViTAL is an application able to supply toxicity alerts at several levels, including genotoxicity with probability values, as well as to furnish molecular fingerprint to increase the confidence of its predictions. The platform leans on a third-part approach which combines the exploitation of SAR/QSAR models and methods based on decision-tree and ANOVA.
Investigates microvascular networks. Vesselucida is an application that can be used to detect modifications that can be relied to brain injuries, strokes as well as diabetic retinopathy and angiogenesis. This program allows users to explore complex 3D images, to rebuild microvascular networks and to produce several metrics including those related to the frequency of anastomoses.
Enables automatic alignment and rebuilding of serial sections, as well as visualization of an entire 3D brain. BrainMaker can generate high-resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes as well as a 3D reconstruction of the entire brain. The software can be useful for cell mapping, cytoarchitectonics and other areas requiring the visualization of neuronal circuitry to create a comprehensive anatomical reference.
Allows imaging, tracking, and analyzing of behavior and movement of Caenorhabditis elegans and other worms. WormLab uses a model-specific tracking algorithm for retrieving data about a single worm or multiple worms, including through omega bends, reversals, and entanglements. The software is able to virtually analyze any video file type. Locomotion data can be exported to Microsoft Excel.
Provides a platform to construct and query compound databases. ChemXplor furnishes a set of functions to create pharmacophoric features, score consensus based molecule profiling and to build large databases. It also includes a search facility, that can be queried by 2D/3D substructures, fingerprints, pharmacophores, receptor or descriptors. This application can be modulated with other software from the same company to enlarge its functionalities.
Enables visualization, storage and sharing of large image data. Biolucida is data management, analysis and visualization system, and a hub for users 2D and 3D image such as 2D/3D slide scanners, confocal Z-stacks and lightsheet whole brain images. Data is stored in a secure and permanent way. The software can be useful for research, medical education, and for publishers. A free application named ‘Biolucida Viewer’, for viewing public images or images shared by collaborators owning Biolucida, is also available.
Permits users to identify and delineate brain regions within experimental brain sections. NeuroInfo yields repeatable, objective anatomic data for understanding the organization and composition of the nervous system. It allows scientists to automatically navigate through the complex microscopic anatomy of histologic sections of mouse brains, eliminating user's potential for error.
Stereo Investigator Whole Slide Edition
Permits users to analyze whole slide image data. Stereo Investigator - Whole Slide Edition is a software tool that performs analysis of cell population number, fiber and capillary length, area and volume of anatomical regions, area and volume of cells, as well as area and volume fraction of Alzheimer plaques. It can analyze image data sets acquired from several scanners and microscopes.
Provides an assortment of features for biomolecule related activities. BioPredicta includes five main features: (i) homology modeling, (ii) protein analysis encompassing analysis such as cavity ranking and identification; (iii) docking, with four different methods including stochastic and manual mode; (iv) GRIP, a ligand-docking methodology that can also be used in protein-peptides and interaction analysis; and (vi) a molecule builder and analyzer including tools for conversion and an editor.
Stereo Investigator Cleared Tissue Edition
Permits users to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Stereo Investigator - Cleared Tissue Edition is a software tool specifically engineered for analyzing cleared tissue image data. This application quantifies numbers of cells, cell volume and surface area, length of branching structures, and region volumes and surface areas.
Enables QSAR modeling and activity prediction. QSARpro predicts activity, allows researchers to optimize leads with insights from QSAR results and generates focused molecular libraries. The software includes multiple 2D/ 3D QSAR methods, VLife's patent pending GQSAR technology for fragment based QSAR approach, a kNN-MFA methodology which creates robust 3D QSAR models, as well as over 40 method options for building QSAR models for prediction of activity and activity-based profiling of a molecular dataset and more than 1000 molecular descriptors.
Assists users with cell mapping, cytoarchitectonics and other areas requiring visualization of neuronal circuitry to create a comprehensive anatomical reference. TissueMaker generates high-resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes. It automatically detects the individual sections on each slide, and then aligns the sections to create the full 3D organ reconstruction.
Assists users in mapping tissue structures. Tissue Mapper is an annotation and delineation tool that can annotate regions of interest from customizable ontology list. It delineates structures at any resolution to create a 3D model from image data. This application also maps images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes
Allows molecular modeling and drug design. VLifeMDS is an integrated platform for computer aided drug design (CADD) and molecule discovery that enables users to perform functions required to pursue structure based as well as ligand-based discovery approaches. The software provides several features, including active site analysis, homology modeling, pharmacophore identification, virtual combinatorial library, docking, QSAR analysis, database querying, virtual screening, and automated workflows.
Enables the study of molecular structure properties assisting in the evaluation and visualization of three-dimensional molecular properties. ProViz Interfaces with VLife Engine and thus provides access to tools for generating graphics for visualizing the properties. It can also generate topographical characteristics. Three dimensional molecular properties which can be studied including those derived from ab initio quantum mechanical wave functions obtained through specialized software programs.
Serves for pharmacophore identification and modeling. MolSign simplifies the pharmacophoric mapping of a molecule by detecting pharmacophoric features such as H-bond donor, H-bond acceptor, positive charge, negative charge and hydrophobe. Additionally, this program embeds features for pattern identification and graphical display of a set of molecules.
Enables and drives ligand-based drug design approach. VLifeQSAR is a high-performance module that allows scientists with an unparalleled level of flexibility to choose from multiple options in data selection through model generation. Users can calculate a variety of descriptors, access multiple methods for data selection, variable selection and either linear or non-linear regression to generate models.
Provides several methods for molecular docking. VLifeDock includes systematic methods and stochastic methods. VLifeDock includes batch docking facility for prioritizing the ligands based on their binding scores. It also provides an array of scoring functions such as piecewise linear potential (PLP) score, XCscore, steric and electrostatic score for evaluation of docked poses.
Permits users to model proteins whose crystal structure is unknown, based on the amino acid sequences of a close homologue. ProModel is a package that allows homology modeling from either a selected template or a user defined template. Users can perform an automated homology modeling simply by reading in the template file or can perform a knowledge based manual modeling by specific loop insertions or by changing specific amino acid residues.
Provides features for molecular modeling functions in the form of force field calculations and conformation generation. VLife Engine has multiple force field options to enable optimization of small molecules as well as macro molecules. It enables expanded scanning of the conformer space through use of a systematic and Monte-Carlo method. It also allows energy calculation and minimization of geometry of molecules using various force fields.
inForm Cell Analysis
Allows quantitative per cell analysis of immunohistochemistry (IHC), immunofluorescence (IF), and RNA in-situ hybridization. inForm Cell Analysis enables the separation of weak and spectrally overlapping markers, in single and multiplex assays. It automates quantitation of biomarker expression from specific tissue types. It includes a module to render immunofluorescence images as hematoxylin and eosin (H&E), diaminobenzidine (DAB) and hematoxylin.
Allows users to perform statistical computation. VassarStats is a web server that offers access to several utilities, including ‘Statistical Tables Calculator’, ‘Convert to Standard Scores’, ‘Data Transformation’, ‘Randomizer’, ‘Estimation of a Sample’s Mean and Variance from Its Median and Range’, ‘Simple Graph Maker’ or ‘Pocket Calculator’, as well as some statistical procedures like ANOVA or ANCOVA.
Permits users to explore, analyze and model small to macro-molecules in a production environment. YASARA Model analyzes contacts, hydrogen bonds, hydrophobic/pi-pi/cation-pi interactions and protein secondary structure. It can measure distances, angles and dihedrals between groups of atoms like helices or planar side-chains. It also aligns small molecules, like ligands, automatically.
Provides support for molecular simulations. YASARA Dynamics includes force fields such as NOVA and YAMBER. Users can employ other molecular dynamics (MD) force fields like AMBER, and run all-atom MD simulations in aqueous solution with Particle Mesh Ewald long-range electrostatics. This application permits researchers to manipulate a simulation interactively and includes features to: (i) pull atoms or entire molecules around, (ii) fix and free atoms, (iii) add restraints, and (iv) toggle force field terms.
Permits users to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials. YASARA Structure can perform twisted structural alignments. This application includes a knowledge-based loop modeler with a compressed index of the PDB, allowing peptide segments spanning selected anchor residues to be located.
YASARA NMR Module
Solves protein structures, based on the protein sequence and distance-, dihedral-angle and residual dipolar coupling (RDC) restraints. YASARA NMR Module is an add-on for YASARA Structure. Folding and refinement are visualized in real-time on screen, allowing the identification of problematic restraints. Floating assignments and non-standard residues are also supported.
Permits users to convert nuclear magnetic resonance (NMR) spectrum data into a 3D structure. YARIA Module integrates the YASARA NMR module with ARIA, a program for automatic nuclear Overhauser effect (NOE) assignment. It also work for CYANA and CNS structures.
BIOVIA Discovery Studio
Aims to optimize drug discovery process. BIOVIA Discovery Studio is a comprehensive suite of science applications. It offers a visualization and collaboration framework that includes a comprehensive science portfolio. It provides several tools for simulations, for macromolecule design and analysis, for antibody development, for structure-based design (SBD), for fragment-based design (FBD) or for pharmacophore and ligand-based design.
Aims to support globally networked drug R&D. ScienceCloud provides an integrated suite of project-centered applications. This cloud-based workspace intends to leverage social communication and allows the: (i) capture and searches of user and application feeds; (ii) post from internal/external systems and; (iii) sharing of crowd knowledge. It also includes the Pipeline Pilot tool that implements standard business rules for partners and also creates and manages scientific protocols.
BIOVIA QSAR Workbench
Permits users to develop, validate and deploy quantitative structure-activity relationship (QSAR) models. QSAR Workbench utilizes native QSAR methods, helping users to reduce costs and to collaborate, by leveraging predictive models. This method intends to reduce the time dedicated to modeling tasks, assists users in making decisions, simplifies model development and reduces errors through a single interface.