Search Results for "gnu make"
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Showing 34 open source projects for "gnu make"
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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... -
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BIGSdb
Software for storing and analysing bacterial sequence data
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. ... -
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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ECOLOG
A database management system for ecological field surveys
ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories. The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics,... -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data... -
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PsPM
A matlab suite for Psycho-Physiological Modelling
PsPM is a powerful tool for psychophysiological modelling. It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although... -
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die... -
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BioRec:Bird Census field data annotation
Recognizing biological data from a notebook.
This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis. -
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We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to a DSS publication. ...
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An open-source implementation of our network-based target deconvolution approach, named target addiction score (TAS). License: The TAS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to the publications below. ...
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A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.
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TUIT
Taxonomic Unit Identification Tool
For the installation instructions please see Wiki page: https://sourceforge.net/p/tuit/wiki/ IMPORTANT: since version 1.0.4.0 TUIT allows to select RDP-like formatted output to improve out of the box compatability with tools, that assume RDP-formatted input. A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section. Read our paper in Biotechniques:... -
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Ezys
Ezys 3D medical image registration program
Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a... -
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The objective of this project is to make available an open-source version of our Multifactor Dimensionality Reduction (MDR) software. MDR is a nonparametric alternative to logistic regression for detecting and characterizing nonlinear interactions.
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RawGeno Version 2.0-1 is released! RawGeno is an R CRAN library automating the scoring of AFLP electropherograms. The library includes a graphical user interface to simplify its use. Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy...
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Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations,... -
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror... -
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Grid Computing MDR
Grid-enabled version of the MDR software
The objective of this project is to make available an open-source of a gridified version of the Multifactor Dimensionality Reduction (MDR) software (http://www.epistasis.org/software.html). -
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Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.
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C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
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GAME stays for Generic Architecture based on Multiple Experts. Its main purpose is to make easy prototyping, test and release of prediction systems. Released by IASC group, university of Cagliari
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This is a utility to convert a set of fasta formatted sequences along with output from ELAND or SOAP (and other next generation sequence alignment in due time) to make them viewable using eagleview.
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PeptideProphet and ProteinProphet CGI program source files modified to make interoperable with Rosetta Biosoftware's Elucidator(R) System. All files are published and distributed under the LGPL license, v2.1.
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The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.
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The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.
