HISTORY

All software were based on MIT Licesensing The project uses Gnu autotools.

This core software bioinformatic package started from 1997 when I was in Charge
of bioinformatic for the Fugu project in The Molecular Sciences Institute. 
Nobody picked up this piece of work. During this time, I wrote code dealing
with the ACEDB, including a C++ driver to this database. The ortholog/paralog
work also started from this period of time. 

July of 2000 I join Neomorphic and started to work on the annotation of the
human genome where I mainly use Java to develope tools and optimize the
accuracy of gene callers.  After neomorphic was acquired, I left Affimetrix and
started a company orpara. In the next few months, there was heavy coding
efforts to build a ortholog/paralog database to be used for multiple purposes.
The objective of the company was to serve small to median sized company in
their needs for bioinformatics with basic tools.  After thorough evaluation of
the business model, we realized that the business enviornment at the moment for
bioinformatic is not mature for service based business model.  

I started working full time for Ferring on GPCR project and designing
Affymetrix chips for discovering drugs related to urinary tracks from 2004.
The main efforts at Ferring is to set up bioinformatics infrastructure, setting
up databases (Postgres), and build web applications to support internal bioinformatics
needs.  Another part of the job it to analyze results from Affymetrix chips.
Orpara code development stop during this period.  

After Ferring closed R&D for drug discovery projects in 2004, I started work
for a financial Institute as a consultant.  The main job is to migrate perl and
C code to other languages.  For the next few months I further developed the
orpara code base before joining the the Joint Genome Institute (JGI) in 2005.
The main componets of the library is to work with sequences and doing alignments
with the sequences. Calculating phylogenetic trees and working with gene models.

At JGI I started working on the genome annotation of eukaryotes. Here most of
the development is in perl. The most important achievments is to have
developped the COMBEST algorithm. The genmodel C++ components were further
enhanced while working at JGI.  All the work done at JGI is funded by the US
govenment and intended to be used by the public. At the end of 2011 I left JGI.
The orpara library was used for some JGI projects and tested.  The gene model
part of the orpara library got further developed.

For the year of 2012 I work as a consultant to develop Java code for migrating
one database schema to another.  And evaluating software packages for
integrating bioinformatics workflows.

From 2013 to 2015 I worked for BMS mainly in helping with using Ion Torrent in
various projects: HCV typing and mutation call, sequencing plasmids (build a
java based web interface for sequenceing and qc) the back end used MIRA 
assembler.  Other projects are for helping TCGA data management, hairpin
RNA analysis. I used the orpara library for these projects.

From Feb to July 2015 I was finshing a paper I drafted around 2011 at JGI.

Since 2002, I host the source code on orpara.com 2 day before Thanks Giving
hard drive hosing the OS died (just little bit over one year, brand new
machine purchased from Dell; I bought several Dell servers over the years
for orpara.com.  This one has the shortest disk life).  This period
coicide with my father-in-laws pass away.  The during Chrismas time
my hand was broken.  I have not find time to brink up the server yet.
Now I am hosting the orpara source in git hub.  

Since July 13, 2015, I started to work for Roche.