For links to current/past members of my group and their interests, please see our lab page.
- Using computers to investigate genomes, their evolution and ecology.
- Developing the statistical bioinformatics tools for this, e.g.
- Developing genomics infrastructure, such as the JBrowse genome browser or the Biomake build tool.
- Synthetic biology, especially RNA engineering.
Computational biology needs realistic, predictive, quantitative models of the how biological sequences --- and systems --- evolve.
My lab develops & applies stochastic process models (e.g. discrete-state continuous-time Markov chains) for the study of molecular evolution.
The dynamics we have modeled include substitutions, insertions and deletions ("indels"), microsatellite dynamics, local duplications, inversions, transpositions, recombinations and rearrangements.
Systems we might consider include sequences, gene families, cis-regulatory networks and chemical signaling pathways.
Ancestral sequence reconstruction
One interest is in paleogenomics: using molecular evolutionary models to make inferences about the origins of life by working backwards from present-era DNA sequences, with the goal of reconstructing those origins in the laboratory synthetically.
Other applications of the models include genefinding, SNP analysis, simulations, and design of combinatorial libraries.
A related interest is "genome ecology": the (evolutionary) interactions of genomes with their neighbors.
Examples include the bioinformatics of transposon classification, virus phylogenetics & recombination, or the metagenomics of microbial communities.
Understanding and re-engineering genomes (and metagenomes) will require a robust set of computational tools.
Computational tools for synthetic biology are also an ongoing interest.
I have an academic interest in several computer-game related areas including interactive fiction, cellular automata, and artificial life (A-life).
In the past I have written several games:
- Zoo Gas (2009) is a cheap and cheerful cellular automaton experiment. Not so much a game, as a very early-stage prototype for a game, experimenting with taking the components of simulations in molecular ecology and polymer physics, and trying to turn them into objects in a virtual world.
- Galactic Dan (1992), with graphics by James Davidson, was published by Fourth Dimension for Acorn's ill-fated Archimedes. Here's a clip on Youtube (here's another). An early, cheap & cheerful first-person shooter/platformer, spiritual descendant of the Wikipedia:3D_Monster_Maze but implemented on a fast RISC chip, it clearly "pales into insignificance" next to Wolfenstein, Doom or Wikipedia:Quake; but some people liked it. In retrospect, the tone we were aiming for was something like Duke Nukem (yes, pretty low). Dan re-appears on several compilations, lately Shootup Games Collection from APDL (review). You can find the cheat codes online.
- Pipeline (1989), co-written with William Reeve, was published by Superior Software for the BBC Micro. It rates a mention on the Wikipedia page for Jupiter's moons in fiction. 8-) Here it is on YouTube. Essentially it was a fast four-way scrolling arcade/puzzle/RPG with a level designer. There's a review here, with a download you can run on an emulator. A PC version, Pipeline Plus, is available from Superior Interactive. In development it was called GuildMaster and I imagined it as a sort of medieval/fantasy guild progression thing, with alternate professions you could follow. My contributions to the code included the non-graphics components: puzzle logic, level designer, etc.
Here are some (mostly retro) games that I've enjoyed over the years:
- Exile: Newtonian physics, implacable robots, synthetic biology, jetpacks, wind, fire, water, grenades, monkeys, mutant maggots, slime molds, bees, fish, an evil genius living in an asteroid... all in 32,768 bytes
- The first game with a "complete physics engine", according to Wikipedia, though "complete" is ambiguous
- Core Wars because programming should be Darwinian
- Not a game I played. But I just love games that are Turing-complete. The Game of Life unit cell is wonderful too
- Elite, The Sentinel and Cholo: atmospheric early 3D. I was the right age to play these
- The first two use procedural generation (as does Exile). Cholo has an intriguing post-apocalyptic thriller plot
- Interactive poetry and fiction.
- UniWar - an iPhone multiplayer turn-based strategy game. Board games in your pocket...
A list of my published papers is here
- Board of directors, Evolutionary Software Foundation
- Skype: ianholmes
- Email: ihh @ berkeley edu
- Office address: 374C Stanley Hall, UC Berkeley, CA 94720-3220
- Office phone: (510) 666 - 2790
- Department: Bioengineering
- Lab address: 381 Stanley Hall, UC Berkeley, CA 94720-3220
- Lab phone: (510) 666 - 2791