Software and Databases
My research has required that I develop and curate a number of databases as well as write software to address the questions that I am interested in. I have done extensive database development in MS Access, FileMaker and MySQL. For software development, I do my coding using Emacs, ConTEXT, and MS Visual Studio.NET. The languages I mainly use are Perl, Visual Basic, SQL, and R/GNU-S. I will use C/C++ on occasion, but I avoid it as much as possible.
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Program: RepMiner: Transposable Element
Data Mining Software Languages: Perl, MySQL Info: SourceForge Project Website Last Updated: Oct, 2009 The RepMiner package takes a graph theory approach to the taxonomic assignment of DNA sequences with a focus on the biology of transposable elements. RepMiner makes use of transposable elements identified from model species to map the location of putative transposable elements onto homology based networks derived from comparing the sequences of the target genome to itself. This package is currently under heavy development. |
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Program: DAWGPAWS : Genome Annotation
Pipeline Languages: Perl Info: SourceForge Project Website Publication: http://www.plantmethods.com/content/5/1/8 Last Updated: June, 2009 DAWG-PAWS is a suite of scripts written in Perl that are desinged to assist a Distributed Annotation Working Group (DAWG) in the sequence annotation of BAC sized contigs. Since this suite of software was initially written to annotate randomly sampled wheat BACs, it is refered to as a Pipeline to Annoate Wheat Sequnces (PAWS). Although these program were initially designed for wheat, the scripts can be applied to nearly any eukaryotic sequence annoation pipeline. |
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Program: BACMan: BAC Data Management Languages: MS Access, MySQL, Visual Basic for Applications and Visual Basic.Net Info: SourceForge Project Website Last Updated: August, 2005 Bacterial Artificial Chromosome Data Management (BACMan) is a Microsoft Access based application designed for the management and analysis of hybridization data related to the high throughput screening of large insert genomic libraries associated with physical mapping projects. |
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Program: BACGrid Languages: MS Word, MS Excel, Visual Basic For Applications Last Updated: January, 2002 This is an automated scoring system for the scoring of dot blot films resulting from hybridization screening of large insert genomic libraries. This software is no longer under active development but anyone else is welcome to take over development of this package. It is a great free alternative to Optical Character Recognition. |
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Program: BACEater Languages: Visual Basic.NET Last Updated: March, 2004 This program will convert scoring grid data from the ABBYY Fine Reader optical character recognition program to the format needed for the BACMan package. This is implemented as a standalone executable. |
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Program: DNA
DABBLER Languages: MS Access, Visual Basic for Applications Download: DNA DABBLER_Dev.mdb Last Updated: March, 2006 A DNA Sequence database that allows for the management of small to medium size databases. This database is suitable for use by beginners in bioinformatics and includes useful functions such as parsers for FASTA formatted text files and conversion between UNIX and DOS file formats. This also includes the Big Dawg BLAST program which provides a graphical user interface to BLAST. |
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Program: OligoMan Languages: MS Access, Visual Basic for Applications Last Updated: March, 2005 The OligoMan database is designed for the management of data related to synthesized oligonucleotides. This database was used at PGML to keep track of nearly 30,000 oligos designed as PCR Primers and overgos. |
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Program: My Genome Collection with
Assigned Taxonomy Languages: PERL, MySQL Info: SourceForge Project Website Last Updated: August, 2005 MyGCAT allows for the management of extremely large sequence database in MySQL. The MySQL database may be interfaced via a set of PERL scripts that allow for automated update of NCBI GenBank database files as well as maintenance of local proprietary sequence databases. All sequence files are taxonomically referenced and an HTML interface allows for the creation of taxon specific BLAST databases. |
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Program: JPerl: Jamie's Perl
Scripts for Bioinformatics Information: Project Home, Downloads, Source, Project Wiki Languages: PERL Last Updated: April, 2007 Various PERL scripts that I have written for processing bioinformatics data as well as general PERL subfunctions that I use. Some of these scripts rely on the bioperl library or have other dependencies that are defined on the project pages. This set of scripts is hosted by code.google. |
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Program: JaRchive: Jamie's R
Script Archive Languages: R Statistical Programming Language Information: Downloads, Source, Wiki Last Updated: April, 2007 A set of Scripts that I have written for the R Statistical Programming Language. This is not an R library, these are scripts that rely on other libraries for the heavy lifting. |
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Program: Visual
Basic Functions For Bioinformatics Languages: Visual Basic for Applications & Visual Basic.NET Last Updated: February, 2005 A number of the visual basic functions that I have written for bioinformatics are here. Many of these are incorporated in my MS Access applications, but I have listed them here separately for others to use in their own modules. |
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Database: LabMan:
PGML Lab Management Database Languages: MS Access, Visual Basic for Applications, gdCom Last Updated: December, 2004 This database allows for inventory management of chemicals, lab supplies, and materials used at the Plant Genome Mapping Lab. The database makes use of barcode labels that are placed on drawers and cabinets throughout the lab to help track where items are stored. This database integrates inventory, an ordering database as well as pipette management. Early editions of this database were developed in FileMaker to allow for cross compatibility with both Macs and PCs. Current development of this database has been in MS Access. Some of the Access code for the ordering database was written by Hash Lala. |
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Database: Southeastern
Endemics Database Languages: MS Access, Visual Basic for Applications, PERL, ArcView 3.x, ArcView Spatial Analyst, Arc Avenue, 3DEM Last Updated: May, 2004 This database of rare plants endemic to the Southeastern United States was compiled in order to test for biogeographic and taxonomic selectivity in the distribution of rare plants endemic to the Southeastern United States. The data resulting from this work has been published in Castanea [1]. |
| Author: James Estill Last Updated: October 15, 2009 |
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