Search Results for "seismic data processing software"
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Showing 31 open source projects for "seismic data processing software"
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. ... -
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools... -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure stable performance during parallel processing. ... -
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels... -
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dataMAPPs
R based pipeline for MHC-associated peptide proteomics (MAPPs) data
dataMAPPs allows routine and efficient processing of data from immunogenicity studies applying the MAPPs peptidomics technology to detect potential MHCI- or MHC-II epitopes as presented by dendritic cells (DC). It features quality control of the raw data, across-sample/across-donor normalization and visualization of results in a heatmap style (heatMAPPs). dataMAPPs' core is a generic R library that can be tailored to specific projects via dedicated control scripts which also allow reproducible recalculation of results. ... -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets.
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HCS Analyzer
High Content Screening Analyzer
HCS Analyzer is an open source software dedicated to High Content Screening data processing and analysis. -
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Protein Microarray Analyser
Protein microarray data processing and normalization
The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. -
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CognitionMaster
object-based image analysis framework
Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34 -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. ... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify... -
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GUDM
A tool for pre-processing and fusing heterogeneous datasets
Global Unified Data Modeler (GUDM) is a bioinformatics software tool used for pre-processing and integrating multiple heterogeneous datasets, collected from multi-modal sources, into an integrated dataset. This integrated dataset is supposed to be used for different types of medical analysis and unified decisions, using different machine learning approaches. -
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xAffect
Sensor Middleware
xAffect is a software framework for online recording, processing and storage of multi sensor data. It was developed at FZI Research Center for Information Technology, Karlsruhe, Germany. xAffect can be used as a flexible, customizable middleware between physiological sensors and applications which require online feature computation (e.g. biofeedback or affective computing). -
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FamSeq
Variant calling on the basis of pedigree information
...FamSeq serves this purpose by providing the probability of an individual carrying a variant given his/her entire family’s raw measurements. FamSeq accommodates de novo mutations and can perform variant calling at chromosome X. To accommodate variations in data complexity, FamSeq consists of three distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. ... -
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q pipeline manager
q: integrated platform for pipeline configuration and management
The q utility is a platform for creating and managing data analysis pipelines. It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently... -
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ELECANS
Electronic Computational Cancer Systems Biology Simulation Studio
A computational model development and simulation environment for cancer systems biology. ELECANS is the state of the art in the multi agent simulation tools available for computational modeling of tumorigenesis in a variety of tissues. -
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ViAmI-Server
Pattern recognition for ADL events
This software uses computer vision algorithms for mining sequence data from telemonitoring data with CBRs. We propose an approach which treats the detection of changes in behavior detected with a sensor/video fusion, which occur at radically different time-scales, through a CBR in two levels: low and high level. The system is always updating the database with the daily data. -
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SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.
