Open Source Perl Data Management Systems - Page 3

EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets. It is designed for scaling beyond Petabytes and 10^13 objects. http://fantom.gsc.riken.jp/4/edgeexpress

EplSite ETL is a tool to do easy the data migrations, doing extraction, transformation, validation and load in a very fast way. It was built by people involved in data migrations so, it contains the necessary to do the migration(Extract Transformation, validation and load) and do it well.

Open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics (thru R), machine-learning algorithms and visualization

The Financial Data Access Library provides an abstraction of market data sources. It verifies data consistency and provides transformation to different time frame e.g. daily to weely. Includes SQL, CSI, ASCII and online data sources such as Yahoo!

Flame graphs are a visualization of profiled software, allowing the most frequent code-paths to be identified quickly and accurately. They can be generated using my open source programs, which create interactive SVGs. See the Updates section for other implementations. Recently I've been helping with d3-flame-graph. The x-axis shows the stack profile population, sorted alphabetically (it is not the passage of time), and the y-axis shows stack depth, counting from zero at the bottom. Each rectangle represents a stack frame. The wider a frame is is, the more often it was present in the stacks. The top edge shows what is on-CPU, and beneath it is its ancestry. The colors are usually not significant, picked randomly to differentiate frames. Flame charts were first added by Google Chrome's WebKit Web Inspector (bug). While inspired by flame graphs, flame charts put the passage of time on the x-axis instead of the alphabet.

Produce a PostScript representation of a project's source code.

FwPlatinum provides real time data analysis of CheckPoint FireWall-1 connection logs. Data is stored for up to 2 years, and is accessed by CGI generated graphs which can drill down to the specific time that you are interested in.

GEOSS: Gene Expression Open Source System (used to be called Genex Va) GEOSS is a secure, multiuser, gene expression database and analysis package. GEOSS is distinguished by a well developed web based user interface, and analysis/reporting.

The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.

Graph handling and layout software developed for helping scientific research. The interface uses Perl, the algorithms are in C++. Creates and shows 3D and 2D graph layouts (several algorithms). Has a scripting interface for graph handling.

GraDiX is a grades data management system specifically designed for handling student grades for teaching institutions. It has many advanced features, making it the perfect solution to grades recording, and dissemination problems.

IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.

ActiveGEM contains a set of perl/Tk graphical interfaces for the GEMPAK meteorological diagnostics and plotting package. These research-oriented interfaces provide easy access to low-level GEMPAK functions and allow for the maximum possible flexibility.

A graphical microcode simulator with a reconfigurable datapath.

Mizore is a suite of evolutionary algorithm tools used to create and simulate artificial neural networks for solving temporally expressed problems.

This project aims to develop a cross platform environment for utilisation of various open source and freely available molecular dynamics and bioinformatics tools. Some extra features are included such as protein hydrophobicity and hydrophilicity plots.

N-Browse is a client-server package for interactive visualization of network data with heterogeneous types of links, intended for ease of use and designed using a generic database schema for data integration and visualization.

OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.

Project moved to https://github.com/ivandeex/optikus

PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create).

We moved to https://github.com/sueswe/pzgtools Perl-Programs to extract information (and visualize them with gnuplot) from data-files from the PZG Particle Sampler from "rr-elektronik" (see http://www.rr-elektronik.de). Linux/KDE-version, GUI written in QT or Gambas. Win32-ver: pzg-tools.npage.de

PentaPlot: A Software Tool for the Illustration of Genome Mosaicism

Comprehensive & high performance data distribution &transformation system. Features a simple, user-friendly event driven scripting interface transparently generates & execs highly efficient Perl/C code. Uses:ETL,datawarehousing,statistics,data-cleansing.

PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.

Pinout is a perl script which makes it easy to produce nice looking postscript ballout/pinout images for BGA or PGA type integrated circuits (IC), ASIC's, FPGA's, or CPLD's.