Open Source Unix Shell Scientific/Engineering Software

MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php

The Airborne Data Processing and Analysis (ADPAA) package is an open-source software package containing a collection of programs and scripts to process and analyze data from in-situ instruments deployed on airborne platforms. The ADPAA package was started to process data on the North Dakota Citation Research Aircraft but has been used to process data on many airborne platforms. The software methodology used in ADPAA is provided in the peer-review publication: Delene, D. J., Airborne Data Processing and Analysis Software Package, Earth Science Informatics, 4(1), 29-44, 2011, URL: http://dx.doi.org/10.1007/s12145-010-0061-4, DOI: 10.1007/s12145-010-0061-4.

Distribuição GNU/Linux brasileira, originalmente para telecentros de projetos de inclusão digital, mas que agora conta com instalação para desktop comum. Distro baseada no Debian GNU/Linux. Foi desenvolvida, primeiramente, para facilitar a instalação e configuração do sistema operacional nos telecentros de projetos de inclusão digital. Conta com programas amigáveis, que são adaptados com com as necessidades de uso, no dia a dia em telecentros ou não.

Please note that OWFS source code, and all Issue/Tickets/merge requests have now been moved to https://github.com/owfs/owfs/. Developer mailing lists will still be kept at Sourceforge. ---- OWFS -- 1-Wire file system. Use the Dallas 1-Wire and iButton chips with standard filesystem commands. Create temperature loggers. Monitor everything. OWHTTPD -- same system, only used as a light weight web server. OWFS is also ported to embedded routers, Mac OSX and Windows. Basically you can use these inexpensive little sensors and other chips with very simple wiring to sense and control the physical environment. The interface is very flexible -- everything from a web browser, to read and writing directly to the chip's "file" to integrating with your programs -- even over the internet. There is a growing number of 1-wire sensors: temperature, voltage, humidity, light, ultraviolet, pressure, thermisters, thermocouples, programmable microcontrollers, relays, lights, LCD panels, etc

Hello, I'm the Aioulinux founder, eager to professionally revive the project. Since 2018, the demand for an IoT and Arduino-tailored environment has been evident. Seeking partners for a 2024 version targeting schools and IoT companies, aiming for a secure and comprehensive platform. If you share this vision and wish to collaborate, reach out. Let's revive Aioulinux stronger than ever! Now seeking partners: Live Distro Specialist: Expert in live distributions to ensure functionality. Marketing Professional: Skilled in marketing to promote and fundraise, with campaign experience. Graphic Designer: Talented individual for the style and layout of the user-friendly Aioulinux. Passionate about IoT and Arduino? Contribute to a secure Linux distribution. Let's collaborate and bring the new Aioulinux to life in 2024! Ready for a project recognized worldwide? Contact me. Let's make a mark together! Today, our distribution includes the following items: ===================

DCMLinux is a complete PACS system, free of charge. Its core is an Ubuntu 14.04 system fully updated and it contains the DCM4CHEE as its PACS server. In the near future it will contain many other addons such as Weasis, Oviyam, Care2x, etc. Just download the iso, burn it to a CD and boot it up. No need to configure any files of dcm4chee, DCMLinux installer asks for everything it needs to configure a running PACS in minutes. Project Wiki : http://wiki.dcmlinux.org Project Forums: http://forums.dcmlinux.org

SimPET (http://www.sim-pet.org) is an open, efficient, and user‐friendly online platform for the generation of synthetic brain PET datasets. The platform offers the ability to generate realistic activity and attenuation maps from patient's PET/CT and MRI images. These maps can then be simulated, and sinograms and simulated images can be downloaded. More advanced features can be obtained by using the SimPET scripts: https://github.com/txusser/brainviset_simset https://github.com/txusser/simpet (New version pre-alpha) You can also upload your own phantoms to simulate. Currently the platform incorporates MC models for the GE Advance, GE Discovery ST and Siemens mCT. More models are on the way. You can also access all the previously simulated datasets from the dev team to test your quantification pipeline (Files section in this page). This project is an open collaboration between IDIS (www.idisantiago.es), Qubiotech (www.qubiotech.es), and FGUMA (www.fguma.es).

This project is for maintaining a linux system that concentrates on math, logic, and geometry related softwares.

SPELL is a framework composed of an integrated environment for the development and execution of satellite automated procedures. It is capable of running any procedure via different Ground Control System and for any spacecraft. The goal of SPELL is to have a powerful and readable automation language, which can be shared across Satellite Operators and Satellite Manufacturers. If we all use the same language, the cost and the risk associated with automated procedures will go down! SPELL facilitates the automation of satellite operations, allowing satellite procedures to be run in a highly repeatable and reliable manner. User manuals provide guidance on the correct use and steps to integrate the software into their existing ground control systems via the well-defined programming interface. SPELL consists of five integral applications which users can use as a complete software suite or as individual standalone applications. Start!: https://sourceforge.net/p/spell-sat/wiki/Home/

MBDyn_sim_suite is a collection of free pre&post-processing tools and simulation models for the open-source multi-body analysis software MBDyn forming a general purpose simulation environment for structural dynamics with an emphasis on wind turbines.

ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract

AICtools is a GIS workflow and set of tools to facilitate Automated Imagery Classification (AIC) and analysis of surface features over time. Allows bulk processing of large data sets, including automated metadata processing/filtering, compressed archive extraction and file manipulation, raster band compositing, pre-processing, mosaicking, clipping. Automates a subset of operations involved in classification of satellite imagery and the associated raster calculations used for time trend analysis.

Provides auxiliary tools for the Monte Carlo particle transport code FLUKA (www.fluka.org).

Aelius is an ongoing open source project aiming at developing a suite of Python, NLTK-based modules and interfaces to external freely available tools for shallow parsing of Brazilian Portuguese. It also includes language resources such as language models, sample texts, and gold standards. Presently, Aelius already offers facilities for POS-tagging and chunking corpora and outputting annotations in different formats, such as in XML in the TEI P5 encoding scheme.

ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.

Benetech Human Rights Program Utility Library: Collection of utilities used by the Benetech Human Rights programming for processing human rights data in preparation for statistical analysis. Library handles DSV files, name canonicalization, binarray, et

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. Please visit the Cloudomics, project for cloud-based resources: https://sourceforge.net/projects/cloudomics-for-aws/

A cooperative passive radar aimed to be used over commercial (and cheap) hardware.

JReferences is a tool to store and retrieve bibliographic references from a file or MySQL database. It reads BibTeXML, DocBook XML and RIS type references, and can output these and BibTex. A bibtex like alternative is also provided for DocBook XML docu

Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat )

MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. * More info + downloads: https://mlpack.org * Git repo: https://github.com/mlpack/mlpack

Malware Analysis Network in Taiwan <Man in Taiwan, MiT> Welcome to contact us (TonTon@TWMAN.ORG) if you are interested in collaborating with us. This project is open source and distributed under the GNU General Public License version 3. Please feel free to add to or modify this source and propose changes or new converters. Developer & Copyrighted by : TonTon Hsien-De Huang Prompter: Jazz Yao-Tsung Wang, Figaro Chen-Ho Yang | Logo Desinger:Temaki Guo Community on Google+：http://X.TWMAN.ORG/Community/ SourceForge: https://sourceforge.net/projects/twmanplus/files/ FaceBook: https://www.facebook.com/TWMAN.PLUS

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es