Open Source PL/SQL 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

The BMF is a Software Framework developed in Java language for the creation of web applications on the server platform also Open source, in clinical, administrative and management for a healthcare company.

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

Talisman is an interpreter for a logical markup language. This language contains the content and logic of a web (or, in the future, Java Swing) based user interface, including arbitrary datatypes and processing actions.

Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. Thus we need to standardize data management and tracking systems, built on a scalable, flexible structure with an easily accessible and web based interface, what is usually called Laboratory Information Management System (LIMS).

This project aim to build a graphical output of BLAST alignments with more then one sequence database. Using Perl scripts and MySQL.

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\".

Cis-Regulatory analysis modules. Includes frequenc/weight matrices scanning at genome level, annotation by using DB access to ensembl, genekeydb, etc. and visualization (through Bioperl or as custom UCSC tracks). May include gene set analysis in future.

Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.

The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.

This software allows us to create a relational database in PostgreSQL hosting full bacterial genomes. Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project. The Cp pangenome delivered to the scientific community fifteen bacterial strains deposited at the GenBank database between the years of 2009 and 2012. The thesis was written in Brazilian Portuguese. However, an English book chapter explaining the software is available at this address: https://doi.org/10.5772/23724. CpDB is the backbone for the Pannotator software: https://pannotator.facom.ufu.br. Both software still is alive and kicking. Enjoy it.

Is an application for management of dengue case data, including basic patient information, clinical information, and laboratory test results, designed for implementation and use in frontline health clinics it includes a geographic management system.

FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

GTdb - Modular genotype database for all markers. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.

LBXR - LOAD BLAST XML RESULTS O sistema permite que sejam importados resultados obtidos por meio de pesquisas de similaridade a partir do BLAST, com resultados gerado no formato XML para o banco de dados relacional MariaDB ou MySQL.

PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format

Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.

Venndiagram comparison for ProteinExperiments in the PRIDE Database

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison. For this purpose it creates a unique workflow integrating third party tools like NCBI Blast or Primer3.

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

The Princeton Protein Orthology Database (P-POD), developed by the Genome Databases Group at Princeton, computes and displays families of orthologs between multiple organisms.

Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

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