Deadlines & Presentation Dates (Group assignments & dates below)


Dec 2  Fri         noon                 Written project reports due

Dec 5,7,8,9      class/lab           Oral Presentations (20')


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


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:


   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 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 1 - Comparison of approaches for determining phylogenetic relationships

        (in turtles & salamanders), including evaluation of high performance computing mechanisms
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

        turkey intestine

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             
        Extra time to finish presentations, if needed