Open Source PHP Bio-Informatics Software

Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab

GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

pISTil (a Pipeline for Interaction Sequence Tag identification and analysis) is a collection of scripts, and programs - running on both Linux and MacOS X systems - for fast analysis of large yeast two-hybrid sequence datasets.

GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.

We wish to develop a personal laboratory information management system for proteomics. LIPAGE is an open source laboratory information management system for 2DPAGE-based proteomics.

S3DB - Simple Sloppy Semantic Database - is a PHP / mySQL,postgreSQL implementation of a local database infrastructure with a semantic architecture. The philosophy of its development is data driven.

Stratos viewer is a web based utility to examine DICOM medical images through a web browser. This project is not active anymore. If you are interested in a Dicom web viewer, have a look at our new development: MedView [ https://github.com/jap1968/medview ]

EDGE3 is an open-source, web-based application allowing for the management, storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform.

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

Controversial ideas of Williamson, Margulis & others suggest speciation by hybridizing might be more common than originally thought. Taking this concept to the nth degree & assuming that indeed, speciation mostly occurs by hybridizing events, not the accumulation of mutations or genetic drift, here is a catalogueoflife2gedcom converter. It allows the tree of life to be displayed as a human genealogy tree with hybridizing events depicted as "marriages." The idea then is that mutation accrual & genetic drift are the determining factors for "species maturation," not speciation itself. Unfortunately the Catalogue of Life Project, catalogueoflife.org, changed its database format more recently, so this converter only works on older versions of the data. In the last working version of the database, making the assumption that each taxonomic name, no matter what level, refers to an original real species & starting them all as female, over 2 million "species/persons" were generated.

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging (http://www.svi.nl/) for parallel batch deconvolutions.

Biological research groups need to store and analyze large amounts of diverse data. LISA (LabInfoSystem:) stores this information in an easily accessible customizable web-based database. LISA requires PHP4 and MySQL. Keywords: Structural Biology, Genomics

A header file (cexcept.h) that provides Try/Throw/Catch macros similar to those available in C++ for error handling.

An interactive data entry, querying, and editing system based on a generic conceptual schema for taxonomic databases. It combines the automated use of scientific names and synonyms in a species checklist with online access to geographical data and common knowledge data (morphological descriptors, genomics, ecology, vernacular names, economic uses, structured notes and conservation status) about the species. All these data can be cross-indexed to a citation list. The design and standard permits rapid customization to suit any taxonomic group.

Ànfàní EHR - an easy to use and electronic health records framework for hospitals and health centers . Th Ànfàní EHR project project was initially created for developing countries, so ease of use was a priority. The basic system which is just for medical records keeping. It offers following features: - Electronic records forms - File uploads - Image uploads - Other media uploads -(audio, video) - Internationalization - Interface translation in English, French, Spanish , Portuguese, Arabic.

Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.

Arrayline is an extensible bioinfomatics data processing platform

BASE is a database server to manage (locally) the massive amounts of data generated by microarray analysis. It handles biomaterials, raw data and images, and provides integrated and plug-in-able normalization, data viewing and analysis tools.

Bantam is a Distributed Annotation System (DAS) server for laboratories with limited bioinformatics support. Bantam keep things simple by using PHP, GFF and a powerful Microsoft Excel spreadsheet for integrated identifier mapping and ontology term lookup

AGENDA (Application for mining Gene Ontology Data)

BioEval, a web-based evaluation platform for one or multiple biomedical text extraction systems and the collaborative creation of gold standards. Handles evaluation of extraction of one to many related entities, plus supporting evidence and normalization

Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions. It strives to provide a comprehensive resource of Protein-Protein interactions for all major species.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.