COSC/BIOL 490 - Cyberinfrastructure
Mid Term Status Report
o In this document we describe the status of the Bluefield State College course
COSC/BIOL 490 - Cyberinfrastructure. This course is being offered for the first time
on the Bluefield WV campus in collaboration with Virginia Bioinformatics Institute
(VBI) in Blacksburg VA. We include some preliminary evaluations in this report.
o This is a hybrid, online and face-to-face, course.
Meeting times: 7:00-8:15 PM, Monday and Wednesday.
Note: beginning the middle of October, this schedule becomes one live meeting per week, the
o The online portion of the course is hosted on CART, BSC’s Center for Applied
Research and Technology, http://ugrad.cartlink.org/user/index.php?id=97
o Credit: 3 hours
o Text: no text was selected for this initial offering of the course.
o The quizzes are delivered online, along with a majority of the assignments.
o Every week students post the results of their work to an online forum. By Wednesday
of each week they post the results of their research and thoughts on a specific
discussion topic, and by Sunday each student has responded to at least two of her/his
o Dr Martha Eborall - Biology
o Dr Lewis Foster – Physics, Natural Science
o Bruce Mutter – Engineering Technology
o Lionel Craddock – Computer Science
o In addition, Susan Faulkner of VBI and Betsey Tretola of the Institute for Distance &
Distributed Learning have instructor access to the course.
Cynthia Barnes Computer Science
Samantha Burchette Computer Science
Josephine Falasinnu Nursing / Computer Science
Dwayne Kimbleton Computer Science
Justin Nichols Computer Science
Dana Olson Post graduate
Keith Solademi Computer Science
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o The Cyberinfrastructure pretest consisted of fifty questions worth one point each. We
had a mixture of questions relating to Biology (Bioinformatics) and Computer Science
(Cyberinfrastructure), with a few concerning Math/Statistics and other disciplines. The
scores ranged from 14.7 to 21.6 with an average of 18.7 / 50.
Lectures / Labs
o Informatics / Bioinformatics Overview - Central Dogma of Life - Genetic Code -
Genomics - Proteomics - Human Genome Project
o Molecular Biology Basics
o Use MUMMER to Compare Genomes and BLAST to Translate a Gene Sequence
o Project Management / Teamwork
o From Gene to Protein - Transcription and Translation
o Pairwise Alignment - Scoring Matrices - Dynamic Programming
o DNA & RNA - Movie: DNA, RNA, and Protein Synthesis - Information to Structure,
~35 minutes running time.
o Genomics – Gene and Protein Prediction
o Explosion of Data / Finding Similar Sequences - D Rainey & S Cammer
o Phylogenetic Analysis - draw phylogenetic tree for different strains of anthrax using
NCBI and Biology Workbench - S Cammer
o Semiglobal and Local Alignments - Smith-Waterman Algorithm - Database Searches -
BLAST - FASTA – CLUSTALW
o Also, we are bringing topical material to almost every class - some examples include
reports on sequencing a macronuclear genome, trends in cyberinfrastructure for
bioinformatics and computational biology, announcement of the awarding of the Nobel
Prize in medicine to Fire and Mello for their work on RNA interference, and testing of
improved polymerases for next-generation sequencing.
See the Appendix for one example of an assignment scoring rubric.
#1 - Read and discuss the NSF report "Revolutionizing Science and Engineering
Through Cyberinfrastructure", commonly called the Atkins report
#2 - Research and discuss the trend towards merging and integrating data
resources in bioinformatics. For example, examine the barriers to and the benefits,
dangers, and consequences of a single worldwide database.
#3 - Use PubMed to research any particular biology topic you desire. Include one
or more Author references and Limits searches. In your Forum discussion relate
new and interesting information you gained from searching PubMed.
#4 - Perform some Web or other research on data searches and pairwise
alignments. Any alignment between two (or more) nucleotide or amino acid
sequences represents an explicit hypothesis regarding the evolutionary history of
those sequences; so, comparisons of related protein and nucleotide sequences
have facilitated recent advances in understanding the information content and
function of genetic sequences. In your Forum discussion describe how sequence
alignments help solve many of the key problems in bioinformatics. Discuss such
questions as: Why might a molecular biologist wish to perform a pairwise
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sequence alignment? A multiple sequence alignment? A sequence database
#5 - This assignment continues your Web-based or other research on data
searches and pairwise alignments. In Assignment #4 you discussed the
motivations for performing these alignments - how sequence alignments help
solve many of the key problems in bioinformatics. Now, research the basic
algorithms and tools for performing these alignments and address how one or
more of the tools or algorithms handle gaps and substitutions in sequences.
Module #1.1 - In your posting due Wednesday, 11 Oct 2006: Identify the hosts of
the Brucella species on p. 13 of your Course Packet for Module 1. Give a brief
description, 25-50 words, of each species. Plus, respond to at least two of your
colleagues by Sunday, 15 Oct 2006.
Intro to PubMed - Use PubMed to research any particular biology topic you
desire. Include one or more Author references and Limits searches. In your
submission relate new and interesting information you gained from searching
DNA (DNA – mRNA – Protein) - Assignment for Extra Credit - Build your own
(should be unique for each student) DNA sequence with 27 base pairs (27
includes the start and stop codons). Show the expected mRNA via the
transcription process. Show the expected protein via the translation process – give
the name, abbreviation, and single letter designation for each of the resulting
amino acids. Possible points: 25
Quizzes have a time limit, usually less than one minute per question. Normally, students
are allowed to take a quiz twice, with the higher score recorded.
o #1 - Quiz on Bioinformatics Overview – average score was 32 points out of a possible
o #2 - Quiz covered material on the Atkins Report, Bioinformatics Tools, and Molecular
Biology – average score was 31.2 points out of a possible 34.
o #3 - Quiz on the Movie, “DNA, RNA, and Protein Synthesis - Information to Structure”
– average score was 42.8 points out of a possible 44.
o Module I: Cyberinfrastructure and the development of a vaccine against Brucella
abortus - Started 4 Oct 2006
Field Trip to VBI - 6 Oct 2006
We and the students were impressed with the staff, facilities and hospitality! Feedback
from the students ranged from very positive to WOW! Our students recognized that the
labs and computational facilities were world class. They were gratified to be able to interact
with the people like Susan, Daphne, Stephen, Oswald, and Bruno.
VBI Visits BSC CI Classes
Two scientists at VBI, Stephen Cammer and Daphne Rainey, made two site visits to the
BSC CI class on September 29 and October 9, 2006. The purpose of the visits was to interact
with both the professors and students and to clarify questions/concerns.
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Some recently gathered feedback from students on their expectations of the course:
o Better understanding of biology and the needs of life scientists so that we can better
support them in our computer science work.
o Develop and enhance team building skills for projects involving scientists from
o Biologists will better understand the complexities associated with and the effort
involved in creating software solutions for their research work.
o Recognition that this was a new, somewhat experimental, course and that the students
are, in a sense, test subjects.
o One student commented that the VBI Field Trip made the course more real world and
provided recognition that we are being educational innovators – the individual thought
“I am really making a difference.”
o Current class is not as diverse in terms of disciplines as we would have liked. One
senior-level Biology student started the course and left after the first week due to his
work load and need to concentrate on graduation requirements. We added the current
offering to the course schedule during the summer – this was too late for many potential
students to change their schedules.
o We focused on the Biology training during the first half of this course. In our next
iteration we will intertwine more tool usage in the four-six weeks of the course; perhaps
we will start one of the Modules much earlier in the course.
o Attendance / Involvement
Overall the attendance and involvement of the students have been good to
One student has experienced transportation problems. He lives more than an hour
away from campus. An inter-county bus is his mode of transportation, and there is
no bus running after 7:00 PM. As a result he is in arrears on his course work.
Dana Olson is a practicing physician from Princeton WV. He has attended the
majority of the class meetings. Because he is the campaign manager for a state
legislator running for reelection, he has missed several recent class sessions. He
expects to participate fully in the class after the election in early November.
Through the second half of the course we will have one live meeting per week -
Structure of remaining class meetings will consist of ½ lectures and ½ laboratory
Lectures will deal with Biology, Cyberinfrastructure algorithms and tools, and
Project Management topics.
Laboratory work will involve the use of BLAST, FASTA, CLUSTALW, and
Module II: Identification of potential drug targets for combating Rickettsia
diseases and potentially multiple pathogenic diseases
Module III: Model Anthrax Strain
Target 3-4 additional quizzes for the course
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Continue with various discussion assignments
Continue with various submission assignments
The pre test questions will be included in the final exam for the course. We will
compare the results of that exam with the pre test.
We are currently considering these texts for adoption for the spring offering of the
Introduction to Bioinformatics, 2/e, Arthur M Lesk, Oxford University
Press, New York, 2005.
Fundamental Concepts of Bioinformatics, Dan E Krane and Michael L
Raymer, Benjamin Cummings, New York, 2003.
We have already listed COSC/BIOL 490 – Cyberinfrastructure in the spring 2007
course schedule. This may address our discipline diversity concern.
We have drafted proposals for making this course part of our regular curriculum.
The proposal title is for COSC/NASC 474 – Cyberinfrastructure, cross-listing the
course in the Computer Science and Natural Science curricula. The faculty of the
School of Arts and Sciences has approved the NASC 474 proposal. The School of
Engineering and Computer Science faculty will address the COSC 474 proposal
at its next meeting. If approved, we will then take the proposal to the Curriculum
Committee of the BSC Faculty Senate.
We (BSC instructors) will devote time from mid-December to mid-January to
firm up content and plans for the spring course offering.
Perform a mid term student evaluation of the course – week of 16 October. Factor
the feedback into the remainder of the class.
o This course has influenced at least two students to reexamine their career tracks. They
have indicated their desire to continue learning about cyberinfrastructure and
bioinformatics - and to pursue internships at VBI.
o We are building this course as we are delivering it. We are in continuous discussion on
the content and delivery of the course material. Our meetings and preparations between
the fall and spring terms will result in significant improvements. Also, we are eager to
develop and improve our skills along with the course.
o In our discussions over the past summer, we had the option of instituting the course for
the fall 2006 or the spring 2007. Bruce Mutter summarized our perspective on the class
in stating that our work this fall will certainly result in a much better offering in the
o We appreciate the support, involvement, and excellent work of Stephen Cammer,
Daphne Rainey, and Susan Faulkner of VBI in this effort.
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Example Grading Rubric
Criteria/points Fail – 0 Meets – 1 Exceeds - 2
Integration of course The posting does not The posting The posting references course
content – reference course references course content and uses relevant
Pts: 4 content content supporting examples that
extend the discussion
Cites 3 references, The posting does not The posting cites The posting cites appropriate
including Atkins report cite the references or appropriate references and utilizes their
Pts: 4 fails to cite them references content as relevant supporting
accurately and according to APA examples of the course
completely style guidelines concepts
Identify the base The posting does not The posting The posting accurately
technologies supporting accurately identify the accurately identifies the base
cyberinfrastructure base technologies identifies the base technologies and provides
services technologies supporting material to explain
Pts: 4 why these technologies are
Response to at least 2 Responses do not focus Responses focus Responses focus
colleagues constructively on constructively on constructively on colleagues’
Pts: 4 colleagues’ postings or colleagues’ postings and give valid
lack valid application postings application of course
of course principles concepts with supporting
references and/or examples
Note: A good resource for the APA (American Psychological Association) formatting guidelines is the
Purdue University Writing Lab & The OWL at Purdue:
We are most interested in how you cite your references. For example, when you cite a Web reference, be
sure to give the date the material was put on the Internet as well as date of access.
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