- In short, Aletheia is software for getting science published and into the hands of everyone, for free. It's a decentralised and distributed database used as a publishing platform for scientific research. So, Aletheia is software. But software without people is nothing. To comprehensively answer the question what is Aletheia, Aletheia is software surrounded by a community of people who want to change the world through open access to scientific knowledge. For a more in depth explanation, Aletheia is an Ethereum Blockchain application utilising IPFS for decentralised storage that anyone can upload documents to, download documents from, that also handles the academic peer review process. The application runs on individual PCs, all forming part of the IPFS database. This gives us an open source platform that cannot be bought out by the large publishers (and any derivitive works must also be open source) that should also be hard to take down due to the database being spread across the globe in multiple legal jurisdictions. Aletheia is designed to be a resilient platform run transparently by the community, not some black box corporation or editorial board, meaning all users can see the decisions Aletheia is making and have a stake in that decision making process if they so desire. By this nature, Aletheia is decentralised, it has no key person risk. Should the core group who invented Aletheia dissapear Aletheia won't cease to exist, it will continue to be run by the community. The community moderates content through various mechanisms (peer review, reputation scores etc.,) to ensure quality of content.
- AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets such as DICOM. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.
- Antidote is an open source implementation of the IEEE 11073-20601 standard. It also contains the implementation of a D-Bus based 11073 manager service.
- BamTools provides both a programmer's API and an end-user's toolkit for handling genome alignment files in the BAM and SAM format. A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data.
- A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.
- BioMail automates searching for recent scientific papers in the PubMed Medline database, and can periodically run a customized Medline search and send all recent matching articles to the user's e-mail address. You can save search patterns: no more remembering which search was good and which wasn't. It is intended for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is also useful for users who have email address but slow or sporadic Web access; they can set up searches and have them emailed to an address instead of having to surf the Web themselves for the information.
- BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.
- The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian. The suggested package enhances the manual pages.
- Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.
- DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come); graphs from every data.
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