Michael Grobe Personal e-mail address: grobe@ku.edu Cell phone:785-218-5252 Current employment: Principle Systems Analyst Research Technolgies University Information Technology Services (UITS) Indiana University at Indianapolis UITS phone: 317-278-6891 My IU web page

This is my personal web site. It is primarily a description of current projects or projects upon which I worked during my tenure at Academic Computing Services at The University of Kansas, but also includes pointers to current interests.

During much of my stay at ACS I managed a group that, for want of a better name, I took to calling the "Distributed Computing support group", which was widely involved in networked computing around campus and even globally.

During the early 90's we built a distributed hypertext system that evolved into the text-based World-Wide Web (WWW) browser, called "Lynx", which was one of the first 4 or 5 World Wide Web browsers ever built and is today available on literally millions of computers worldwide. (For a more complete history of the early devlopment of Lynx see: http://people.cc.ku.edu/~grobe/early-lynx.html.)

Around the turn of the millenium, I got an urge to begin a fairly detailed description of my own work at KU.

My current (circa 2007) interests and activities include:

• molecular biology, in general, and Systems Biology and Synthetic Biology in particular:
  • the simulation of cell signaling pathways
  • Using Detrended Fluctuation Analysis (DFA) to identify exons

  • Some test interfaces to genomics data done at Indiana:
    • Get SNPs in a specified human chromosomal region using NCBI eSearch and eFetch
    • Get NCBI sequences for genes or specified regions
    • Find endogenous repeat sequences within a sequence
    • Send SQL commands directly to dbSNP via CGI, Java, and JDBC
    • Get a comprehensive list of a SNP's neighbors
    • Get a comprehensive list of SNPs within a chromsome region

  • Documentation related to using dbSNP and the NCBI eUtils:
    • Using the relational and eUtils interfaces to dbSNP
    • Using dbSNP via SQL queries
    • Using the NCBI eUtilities via CGI

• Grid-related technology, especially as it applies to the TeraGrid:
  • Making relational data available over the Grid: A survey from CGI to OGSA-DAI
  • Using WSRF to build workflow scripts: Temp "files" and filters in a Grid environment

• network-based collaboration systems, including the development of:
  • an Evaluation of the Marratech video-enhanced collaboration system
  • a web-based service to help coordinate virtual meetings (To see a prototype click here.), and
  • An introduction to networked media concepts and services.
  • a short tutorial on video compression called Notes on video compression and compression standards

• looking for patterns related to chaotic, and/or scale invariant, behavior in Internet traffic, DNA sequences, and other dynamic processes. See:
  • Searching for patterns in the Netometer and Webometer archives,
  • Using Detrended Fluctuation Analysis (DFA) to identify exons, and
  • Characterizing archived Netometer and Webometer data with respect to power-law distributions and fractal dimensionality,

• recent programming projects
  • interfaces for accessing the Centralized Life Sciences Data (CLSD) service (using Java, Perl, Web Services (JAX-RPC), the Web Services Resource Framework (WSRF), AJAX, etc.),
  • Using the NCBI eUtilities via CGI,
  • the Java object model, as described in Java objects without adornment, which attempts to separate the basic ideas comprising the Java object model from various language features that may obscure it. (The use of some Collection classes is also described.)
  • Using the Linden Script Language (LSL) within the SecondLife virtual environment
  • some utility routines I put together, mostly for looking at time series patterns. There exist analogs for many of these programs that operate on Netometer and Webometer archive data.

• Some miscellaneous interests
  • the construction and use of portals using such tools as Tomcat, uPortal, and WSRF containers (both Perl- and Java-based).
  • the structure of web-accessible database systems and archives for digital media, such as the Digital library archive system (DSpace) at KU.
  • authentication processes, as in An instantaneous introduction to authentication using Argus.
  • inspecting disease gene-protein networks.