The following selected industry software projects were all
developed directly by or under the technical supervision of Russell
Turner.
Atavist
Designed and implemented Atavist,
an
interactive
Java-based research tool for viewing and analyzing comparative genomics
data. Displays multiple genomic axes together with aligned genomic
features. Also displays syntenic relationships, alternate splice graphs
and dot-plots as well as histograms. Visual appearance of genomic
features can be controlled by the user through type attributes.
Atavist
- comparative view of human and mouse RefSeq orthologs
Atavist - ESTs mapped to human
genome sequence
Atavist - display of alternate
splice graph for a human gene
Atalanta
Designed and implemented Atalanta, a
Unix tool
written in C++
to project genomic feature coordinates between different genome
assemblies of the same or closely related species. Used as a component
in the AIR pipeline for computing gene annotations on Celera’s
Rat genome sequence. Projections are based on assembly-to-assembly
mapping data generated by the A2Amapper mapping tool.
Atalanta
- diagram of the genomic feature projection process
Atalanta - mouse/rat ortholog
exons projected across cDNA and genomic sequence
Genome Browser
Technical lead responsible for software design and
development of the CeleraGenome Browser,
an interactive Java-based 3-tiered application used by Celera
scientists and customers for visualizing and annotating genomic data,
including Celera’s human, mouse and rat genome databases. The front-end
is a
high-performance "thick" client which loads serialized Java objects on
demand from an EJB-based middle tier running in a WebLogic
application server, hitting an Oracle database backend. The client is
constructed using a standard MVC software architecture, and users can
integrate their own data with the database data by loading XML files
into the client model. Annotation is performed via interactive "drag
and drop" creation and editing of annotation features with
infinite-level undo. Developed using JDK1.3, Jbuilder
and TogetherJ development tools.
Genome Browser - display
of features on rat CFTR region
Genome Browser - CFTR
transcripts of nine species projected onto human genomic sequence
Genome Browser - feature detail
on human chromosome 1 showing alignment view Slide Presentation: [PowerPoint][HTML]
LCMS Viewer
Designed and implemented LCMSViewer, a prototype research
tool for viewing liquid
chromatography mass spectrometry data. It displays data as a 3D height
field with interactive pan and zoom capabilities. Data is loaded in
progressively from a hierarchically formatted file as user zooms in,
allowing large datasets to be viewed on small memory machines. Written
in Java using the Swing and VTK graphics
packages.
LCMSViewer - feature detail showing elusion profile and isotope cluster
MSMSViewer
Responsible for full life-cycle design and
development
of the MSMSViewer,
an interactive Java-based 3-tiered application for viewing and curating
tandem mass spectrometry data from Celera’s proteomics pipeline. It
consists of a front-end based on Swing and Sitraka JChart
graphics APIs, an EJB-based middle tier running in a JBoss
application server, and an Oracle database backend. Developed using JDK1.3,
JBuilder and MagicDraw development tools.
MSMSViewer -
Scope view showing fragment peaks and peptide predictions
MSMSViewer -
Peptide fragment view showing all theoretically possible peptide
fragments
JGraphics
Responsible for concept, design, major
implementation
and documentation of JGraphics,
a Java-based visual software development system for building
interactive data-driven dynamic graphics displays with little or no
programming. Utilizes interactive iconic programming methodology
similar to JavaStudio. Displays can run as web applets,
standalone applications or JavaBeans. Developed on Windows
and Linux platforms using JDK1.1, Symantec
Café and JBuilder development tools. Full
hierarchical vector graphics functionality built on top of AWT
drawing model. Dynamics implemented by specialized dataflow propagation
algorithm incorporating lazy evaluation. Imports and exports JavaBeans
with data connectivity to sockets and JDBC via SQL.
JGraphics
- creating a dynamic drawing for displaying real-time stock data Slide Presentation: [PowerPoint][HTML]
Russell Turner, Ph.D. 
