Deadlines &
Presentation Dates (Group assignments & dates below)
Dec 2 Fri
Dec 5,7,8,9
BCB 544 Project
Report: Oral portion
1. Each oral presentation will be 20' long; with 5'
for questions (we will use a timer)
2. Every member of each group must speak, but different
students may speak for different lengths of time
3. Each oral presentation will be a PPT presentation with 20
slides (or you may use HTML if you prefer)
4. Each group will be responsible for providing the
PPTs to Drena or David (depending on whether you prefer Mac or PC ;-)) at least
1 hour prior to the presentation. We will provide a USB drive to
facilitate this.
BCB 544 Project
Report: Written portion - Content
Each project report should include:
1. Title of project
2. Names of project members
3. Biological problem investigated (background
& significance, question or hypothesis addressed)
4. Computational issues addressed
(explain what new algorithm/tool you developed OR what available tools you
used/modified in order to address your biological question)
5. Relationship between the project and
the topics covered in class (this can be
stated in a couple of sentences in the "Acknowledgements" section of
your paper - see below)
6. Conclusions (What do your
results mean? Did they answer the question you set out to answer?
What is the significance of your results? of the
new tools or new application of available tools presented in your work? What
are next steps/future directions?
Regarding # 5, we expect each project to touch upon one or
more course subjects. This does not mean, however, that students
can only use techniques covered in class.
BCB 544 Project
Report: Written portion - Format
David & I agreed that it would be most useful for you to
write your project report in the format of a manuscript for submission to the
journal Bioinformatics. This will be great practice for you, makes
our task of fairly comparing projects easier - and who knows - perhaps this
will be a first draft of a paper you will actually submit!
Our expectations are:
1. Each group will prepare a single manuscript in
Bioinformatics format
http://bioinformatics.oxfordjournals.org/
2. Papers will adhere to the guidelines for one of
two types of papers in Bioinformatics, either
"Original Paper" or "Discovery Note" (see
brief descriptions provided below & examples in the journal).
The items listed under "Content" above should be incorporated into
standard manuscript sections described below. For #5 above (relationship
to topics covered in class) - incorporate your answer into the "Acknowledgements"
section.
3. Papers will not exceed 3000 words (regardless of
whether "Original Paper" or Discovery Note")
4. Papers will be formatted according to the requirements described here:
http://www.oxfordjournals.org/bioinformatics/for_authors/general.html
4.1 Follow
the instructions under "Manuscript Preparation" at above
website (scroll down!) & include appropriate sections, e.g.,
structured abstract, introduction, system or methods, algorithm,
implementation, results, discussion, references.
4.2 Place each Figure or Table, together
with its legend, on a separate page at the end of the text (i.e., don't
spend time trying to insert figures into text portion of manuscript).
NOTE: It is NOT necessary (or
even desirable) to use the Word.dot or LATEX "templates"
provided. We want you to spend time on content, not formatting.
5. Papers will be submitted both electronically (to
both David & Drena) and in 1 hard copy to Drena.
6. Supplemental information may be provided online.
Include the URLs in your manuscript.
>> Additional
information re: two types of Bioinformatics
papers:
Original
Papers (up to 3000 words
(not 5000 per journal instructions)
Original
papers that describe new research developments in computational molecular
biology, for example: models, algorithms, software involving new methods,
biological databases and network information services, and their impact on
molecular biology or computer science. Actual biological data, as opposed to
purely simulated data, must be used. (You may use simulated data for this project!)
Discovery
Notes (up to 3000 words)
Discovery
notes report biologically interesting discoveries using computational
techniques. Topics may include sequence motif detection, definition of new
domains, structural similarities, gene structure prediction, comparative
genomics, biomolecular networks and other aspects of computational molecular
biology. The results presented should present new discoveries, bringing insight
to a relevant biological problem, and not be the simple extension of current
knowledge. The results are expected to proceed from the specialized use of
tools, methods, and databases. The inclusion of experimental results is
considered very positively.
Groups &
Presentation Schedule:
Group 1 - Benmjegerdes, Carroll, Deitloff, Myers
Group 2 - Gottimukkula, Muraoka
Group 3 - Couture, Romine, Wagner
Group 4 - Jones, Hecker, Nielsen,
Group 5 - Brathwaite, El-Manzalawy, Kohutyuk, Stavarche
Group 6 - J Ding, Liu, Natarajan, Wang
Group 7 - Y Ding, Zhao
:
Dec 5 Mon
Group 6 - Phylogenetic relationships among Rec A gene family members, esp. in
maize
Dec 7 Wed
Group 2 - Identification of genetic differences that
determine ability of Campylobacter strains to colonize
Group 3 - Identification of genes that restore
complement-resistance in attenuated Leishmania strains
Dec 8 Thurs
Group 4 - Microarray & functional genomics analyses of
phenol-induced proteins in Pseudomonas
Group 5 - Proteomic & functional/structural genomics
analyses of proteins expressed in developing retina
Group 7 - Bioinformatic analyses of Lipcalin 2: structure,
function, phylogeny
Dec 9 Fri