BOSCVienna, Austria

July 20, 2007

Kam D. DahlquistDepartment of Biology

John David N. DionisioDepartment of Electrical Engineering

& Computer Science

Loyola Marymount University

An Open Source Frameworkfor Teaching Bioinformatics

Outline

• Motivation

• Open source culture

• Implementation--Computer science curriculum--Bioinformatics course

Scientific Computing and the Digital Divide

Wilson GV (2006) Where’s the real bottleneck in scientific computing? American Scientist 94:5–6.

Scientists who come to computer science after being trained in a different primary discipline often have to rediscover, relearn, or keep up with work in the computer science and software development realms in order to get the most out of their work.

This causses unecessary and unknowing repetitions of past discoveries and errors.

Tools or paradigms that are out-of-date in computer science and software engineering remain in place.

At worst, software flaws slow or impede research.

Baxter SM, Day SW, Fetrow JS, and Reisinger SJ (2006) Scientific software development is not an oxymoron. PLoS Computational Biology 2:e87.

The Disconnect Between Undergraduate Computer Science Training and Expectations and Skill Sets

Required for Industry and Research

Undergraduate Training

Industry Expectation

Work alone Work in a team

“Toy” programs and algorithms

Large, modular project

Throwaway code

Code longevity (for better or

worse)

inroads – The SIGCSE Bulletin, Volume 39, Number 2, 2007 June, pp. 70-74

http://recourse.cs.lmu.edu/

Official Open Source Definition (version 1.9)

Free redistribution

Source code

Derived works

Integrity of the author’ssource code

No discrimination againstpersons or groups

No discrimination againstfields of endeavor

Distribution of license

License must not bespecific to a product

License must notrestrict other software

License must betechnology-neutral

Open Source Values

• Source code is available, modifiable, and long-lived

• Accountability implies community--explicit “paper trail” for how a particular program changes over time--communication and answerability

• Responsibilities accompany rights--explicit consideration of the license--giving credit where it is due--appropriate access to software, documentation, and communities--acknowledging security, privacy, legal issues

Open Source Teaching Framework

Source Code:• All code resides in a centralized, public repository• As much as possible, everyone’s code is visible to everyone else for code review or team fixing• No code is thrown away, it remains available to future “generations”

Open Source Teaching Framework

Source Code:• All code resides in a centralized, public repository• As much as possible, everyone’s code is visible to everyone else for code review or team fixing• No code is thrown away, it remains available to future “generations”

Quality & Community:• Documentation, inline and online• Automated tests• Constructive code review, beyond “does it work?”• Long-term projects release early, release often• Form collaborative communities among faculty, students, classes, and projects

Progression through Computer Science Curriculum

• Sample code bazaar--the creation and maintenance of live, organized, searchable, student accessible sample code libraries--students check out, modify, and check in code

• Test infection (Erich Gamma)--test suite vs. implementation matrix

• Life cycle of code--as juniors and seniors, students revisit code written the first year--direct experience with need for documentation

• Release early, release often--applies to both students and faculty

“CourseForge”A Hardware + Software Infrastructure

for Supporting the Teaching Framework

• Certain teaching elements are impractical without some degree of automation

• Support platform for management of student work --revision control --test frameworks --communication --issue tracking

• Derived from open source software, delivered as open source software — the system will interoperate with existing open source tools

CMSI 698: Special Studies in Bioinformatics

• Team-taught by a biologist and a computer scientist

CMSI 698: Special Studies in Bioinformatics

• Team-taught by a biologist and a computer scientist

• Enrollment in Spring 2006: -- eight students from Master’s degree

program in Computer Science -- several coming from aerospace industry-- none with more than college-level introductory biology

CMSI 698: Special Studies in Bioinformatics

• Team-taught by a biologist and a computer scientist

• Enrollment in Spring 2006: -- eight students from Master’s degree

program in Computer Science -- several coming from aerospace industry-- none with more than college-level introductory biology

• Project-based class began development of XMLPipeDB

CMSI 698: Special Studies in Bioinformatics

• Team-taught by a biologist and a computer scientist

• Enrollment in Spring 2006: -- eight students from Master’s degree

program in Computer Science -- several coming from aerospace industry-- none with more than college-level introductory biology

• Project-based class began development of XMLPipeDB

• XMLPipeDB development continued by four students in summer session course entitled Open Source Software Development Workshop

CMSI 698: Special Studies in Bioinformatics

• Team-taught by a biologist and a computer scientist

• Enrollment in Spring 2006: -- eight students from Master’s degree

program in Computer Science -- several coming from aerospace industry-- none with more than college-level introductory biology

• Project-based class began development of XMLPipeDB--authentic bioinformatics problem to solve

• XMLPipeDB development continued by four students in summer session course entitled Open Source Software Development Workshop

• One student continued development for Master’s thesis

XMLPipeDB Project Management: Lessons Learned

• Students on the project had varying levels of maturity, knowledge, and skill coming into the project

-- some naturally took on a leadership role-- some hung back or did the minimum required to get by

XMLPipeDB Project Management: Lessons Learned

• Students on the project had varying levels of maturity, knowledge, and skill coming into the project

-- some naturally took on a leadership role-- some hung back or did the minimum required to get by

• Needed to increase communication and sense of team-- students preferred to interact with faculty for questions, rather than each other-- bug trackers and developer’s forum used only sporadically-- implemented weekly reports on Wiki to increase accountability

XMLPipeDB Project Management: Lessons Learned

• Students on the project had varying levels of maturity, knowledge, and skill coming into the project

-- some naturally took on a leadership role-- some hung back or did the minimum required to get by

• Needed to increase communication and sense of team-- students preferred to interact with faculty for questions, rather than each other-- bug trackers and developer’s forum used only sporadically-- implemented weekly reports on Wiki to increase accountability

• [SourceForge servers were frequently down during class]

XMLPipeDB Project Management: Lessons Learned

• Students on the project had varying levels of maturity, knowledge, and skill coming into the project

-- some naturally took on a leadership role-- some hung back or did the minimum required to get by

• Needed to increase communication and sense of team-- students preferred to interact with faculty for questions, rather than each other-- bug trackers and developer’s forum used only sporadically-- implemented weekly reports on Wiki to increase accountability

• [SourceForge servers were frequently down during class]

• 6 months from conception to product

XMLPipeDB Project Management: Lessons Learned

• Students on the project had varying levels of maturity, knowledge, and skill coming into the project

-- some naturally took on a leadership role-- some hung back or did the minimum required to get by

• Needed to increase communication and sense of team-- students preferred to interact with faculty for questions, rather than each other-- bug trackers and developer’s forum used only sporadically-- implemented weekly reports on Wiki to increase accountability

• [SourceForge servers were frequently down during class]

• 6 months from conception to product

• Even the weakest student contributed useable code

Take-home Messages

• Catch them early

• Making open source values and software development best practices explicit will produce better software and better computer scientists

XSD-to-DBXSD-to-DBAdam CarassoAdam CarassoJeffrey NicholasJeffrey NicholasScott SpicerScott Spicer

XMLPipeDBUtilsXMLPipeDBUtilsDavid HoffmanDavid HoffmanBabak NaffasBabak NaffasJeffrey NicholasJeffrey NicholasRyan NakamotoRyan Nakamoto

UniProtDBUniProtDBJoe BoyleJoe BoyleJoey BarrettJoey Barrett

GODBGODBScott SpicerScott SpicerRoberto RuizRoberto Ruiz

GenMAPP BuilderGenMAPP BuilderJoey BarrettJoey BarrettJeffrey NicholasJeffrey NicholasScott SpicerScott Spicer

Special ThanksGenMAPP.org Development GroupCaskey L. Dickson, Wesley T. CittiNSF CCLI Program (http://recourse.cs.lmu.edu)

http://xmlpipedb.cs.lmu.edu

LMU Bioinformatics Group

Kam D. Dahlquisthttp://myweb.lmu.edu/kdahquikdahlquist@lmu.edu

John David N. Dionisiohttp://myweb.lmu.edu/dondidondi@lmu.edu