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Learning About Bioinformatics at the Community College

Bioinformatics requires the "wedding" of biology, mathematics, and computer science.

Bioinformatics studies must support at least three student types.

• no computer literacy; no biology (newbie)
• biology literate; does not compute
• computer literate, but no biology

The course sequences presented in this document emphasize the computing component of bioinformatics. Given the difficulty of teaching bioinformatics at community/junior colleges, the course sequences are designed such that after two-years of study a student has developed a computing foundation that offers them numerous choices.

• The student can enter a four-year bioinformatics degree program.
• The student can enter a four-year computer science degree program [and, potentially, other computer-related degree/certificate studies].
• The student can become an entry-level (newbie) computer professional.
• If the student is a computer professional, then they have updated their computing skills and have positioned themselves to stay a computer professional.
• If the student is a professional in a field other than computing, then they are positioned to re-career into the computing profession.

Course Sequences

Two-Year Pre-Bioinformatics Newbie Program [60 credits]

Semester One

biology I
math I
english I
internet I       + email, usenet, ssh, sftp, www, XHTML, CSS, SSI
unix I           + command-line, files/directories, IO, pipes, text editor

Semester Two

biology II
math II
english II       + technical writing emphasis
internet II      + websites, XML, collaboration tools (intro)
unix II          + first programming course using bash

Semester Three

biomath III      + math III/biology III
C                + C (entire language; STDC Library)
software engineering  + structured, object, generic, extreme
unix III         + make; cvs; basic SysAdmin; ApacheAdmin; sys/web programming 
digital design   + hardware (devices)

Semester Four

biomath IV       + math IV/biology IV
C++              + object-oriented/templates; data structs/algorithms
Perl and Python  + object-oriented; data structs/algorithms; REs
database I       + relational (SQL) and others
assembly         + general; c/c++ executing assembly

Two-Year Pre-Bioinformatics for Biologists [60 credits]

Semester One

biomath IV       + math IV/biology IV
internet I       + email, usenet, ssh, sftp, www, XHTML, CSS, SSI
unix I           + command-line, files/directories, IO, pipes, text editor
software engineering  + structured, object, generic, extreme
database I       + relational (SQL) and others

Semester Two

internet II      + websites, XML, collaboration tools (intro)
unix II          + first programming course using bash
bioinformatics I + biotools (software); biodatabases
digital design   + hardware (devices)
C                + C (entire language; STDC Library)

Semester Three

C++              + object oriented and generic programming
Perl and Python  + object oriented; data structs/algorithms; REs
unix III         + make; cvs; basic SysAdmin; ApacheAdmin; sys/web programming 
collaboration tools   + mailing lists, wikis, slashdots, sourceforge 
markup languages + XML/BIOML; DTDs/Schemas; semantic web

Semester Four

software engineering II         + the practice of programming
artificial intelligence/machine learning
computer simulation/visualization/graphics
datamining    

???-Year Pre-Bioinformatics for Computer Professionals [?? credits]

The course of study for these students depend upon their computing backgrounds; they take the computer classes they are deficient in. Their course of study also depends on their math and biology backgrounds. In many cases, the student should start at the beginning as if they were a newbie.

Computer professionals who start the program at the beginning do so as if they were a graduate student in an under-graduate course.

Informatics Only Component of Bioinformatics

Bioinformatics includes the professions of System and Network Administration. Bioinformatics requires secure and reliable computing systems; however, the course sequences presented in this document do not produce System Administrators.

Here is a hyperlink to the System Administration course sequences. [http://deru.com/~gdt/biotech/curriculum/sysadmin.html]

Inclusion of Assembly Language; Potential Alternate

Assembly language with C linkage added to satisfy ASU CS/CSE degrees. Non-CS students could take Software Engineering II. SEII uses The Practice of Programming which has the following table of contents: style, algorithms and data structures, design and implementation, interfaces, debugging, testing, performance, portability, notation. This follows the first software engineering course taken during the previous semester. Most source code examples are in C, which was learned last semester. Students get exposure to Java. Data structures and algorithms used in two other classes.

About Biology I and Biology II

The following is from Dr. Suzanne Kelly at SCC.

"Regarding the two biology courses, I think that the BIO 181 and a modified BIO 245/246 would fit. The modifications would mean that the course would focus on molecular and cellular biology for both lecture and labs. The existing BIO 245/246 used by MCC for its Biotechnology program is too much like BIO 181."

Computing Ethics and Computer Security

Every computer course includes a section on computing ethics and computing ethics only. Bioinformatics requires a merging of ethics from multiple disciplines.

Communication Skills

Communication skills are practiced in every course.

Author: G.D.Thurman [gdt@deru.com]
Created: 11 Mar 2003