Open Source PHP Bio-Informatics Software

Open Information Systems for Emergency Services (Open ISES) is a community of software developers, paramedics, EMTs, law enforcement & fire fighters working together to create open source software & training materials for the emergency service community.

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

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

* 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 using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file

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

Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk

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.

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.

OpenCare is an easy-to-use, feature-rich, extremely expandable, research-oriented Electronic Medical / Health Record System (EMR/EHR) written in PHP currently using MySQL as a backend.

PHP-PBS, is a Graphical Interface to PBS written in PHP. It should work on all Linux platforms with apache and a MySQL database.

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.

This project is the implementation of The Virtual Collaborative Environment (VCE) which supports clinical applications of 3D modeling in medicine. The system is based on three layer client-server architecture.

bioGraph is a set of PHP scripts which can be used in enzyme assays. Currently, this includes pH, Temperature, Michaelis-Menten and Lineweaver-Burke plots.

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

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.

The project aims to extend the PHP scripting language to enable PHP developers to write bioinformatics applications more rapidly than if they had to start from scratch using \"vanilla php\".

It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.

birdweights is a a package of scripts to analyze data from an automated system for the measurement of mass and identification of birds at perches.