"CreateEpitome" is an interactive program (created via Silverlight) and a command-line program for Windows.
Given a weighted set of amino-acid sequences, it creates a new amino-acid sequence that covers input sequences. It works step-by-step, producing an output line after each step. The possible steps include:
- Combining two input sequences that overlap
- Adding an input sequence to an output component with which it overlap
- Combining two output components that overlap
To achieve reasonable efficiency, the program
- Works in a heuristic, greedy fashion. It always takes the best next move without considering how that affects future moves.
- Keeps up-to-date lists of all candidate moves and their value. When a move is made, it updates the list of candidates efficiently, avoiding complete regeneration.
- Command-line version runs on multiple processors, if they are available.
D. Yerly, D. Heckerman, T. Allen, T. Suscovich, N. Jojic, C. Kadie, W. Pichler, A. Cerny, C. Brander. Design, expression and processing of epitomized HCV encoded CTL epitopes.
, to appear.
D. Nickle, N. Jojic, D. Heckerman, V. Jojic, D. Kirovski, M. Rolland, S. Pond, J. Mullins.
Comparison of immunogen designs that optimize peptide coverage: Reply to Fischer et al.
PLoS Computational Biology
, 4(1):e25, January 2008.
D. Nickle, M. Rolland, M. Jensen, S. Pond, W. Deng, M. Seligman, D. Heckerman, J. Mullins, and N. Jojic.
Coping with viral diversity in HIV vaccine design
, PLoS Computational Biology
, 3(4): e75, April 2007.
N. Jojic, V. Jojic, B. Frey, C. Meek, and D. Heckerman.
Using epitomes to model genetic diversity: Rational design of HIV vaccine cocktails
. NIPS 2005.
Pre-Compiled Programs for Windows
- Run by selecting "Start" and "Create Epitome"
Source Code Files
(To download see
Source Code tab
- Solution file: CreateEpitome\CreateVaccine\CreateEpitome.sln
- Build directory: CreateEpitome\CreateVaccine\CreateEpitome\bin\Release
Compiling the project requires
Some source code features of possible interest:
How to run regression tests
- Builds both Silverlight and .NET versions from the same C# code in the same Visual Studio solution.
- Includes installer that installs both versions including setting up the Silverlight version to run locally.
- The Silverlight version resizes the Silverlight control on the web page.
- The Silverlight version shows results interactively as they are produced. It allows the run to be paused and continued. It plots the performance of the algorithm.
- The command-line version runs multi-core, if available.
- The Silverlight control appears in an HTML table and is visable to both IE and Firefox.
- The code uses the HashSet data structure. For Silverlight, where HashSet is not available automatically, a mini version is provided.