Deadlines
& Presentation Dates (Group assignments & dates below)
Presentation Schedule:
Wednesday,
Dec 5th
Friday,
Dec 7th
IMPORTANT!
All
Students (444 & 544)
are required to attend all BCB 544 project presentations next week - attendance
will be taken!
HW#7:
Project Presentation Evaluations
Total of 4
forms, due in class, immediately after each presentation
BCB 544 Project
Report: Oral portion
1. Each oral presentation will be 25-30' long; with 10' at end
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 < 40 slides (or you
may use HTML if you prefer)
4. Each
group is responsible for providing PPTs to Drena or
Michael (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.
5.
Here is a presentation
for how to give a good talk by Simon Peyton Jones.
6.
The seminar
evaluation form is available to give you an idea of what criteria will be
used to evaluate your presentation.
BCB 544 Project
Report: Written portion - Content
Each written project
report should include:]
1. Title
of project
2. Names
of project members
3. Biological
problem investigated (Introduction, Background & Significance, State the
Question, Hypothesis or Problem addressed)
4. Computational
issues addressed (Explain what new algorithm/tool you developed OR
what available tools you used/modified in order to address the biological
question)
5.
Results (Concisely summarize your results, use Tables &
Figures to present data.)
6. Conclusions
& Significance (What do your results mean? Did you answer the
question you set out to answer? What is the significance of your results or
of the new tools or of the new results obtained using available
tools presented in your work? What are next steps/future directions?
7.
Authors' Contributions (What did each team member do? Whose
idea was the project? Who did the programming? Who ran the
experiments? Who analyzed the results? Who wrote and/or proofread
the report? Who prepared the PPTs slides? etc.)
BCB 544 Project Report: Written portion - Format
We believe it will 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, with papers adhering to
guidelines for “Discovery Note” papers in Bioinformatics - except
that the number of Tables and Figures is not limited to 1 or 2. See
brief description provided below & examples in the journal.
2.
Papers will not exceed 3000 words
3.
Papers will be formatted according to the requirements described here:
http://www.biomedcentral.com/bmcbioinformatics/ifora/
4. Items 1-7 listed
under "Content" above should be incorporated into standard
manuscript sections:
Title page
Abstract
Background
Results
Discussion
Conclusions
System and Methods (datasets, software, algorithms,
implementation and/or biological system, experimental methods)
Authors' Contributions
References
4.1 Follow the instructions under
"Preparing main manuscript text" at above website for formatting
instructions for references, etc.
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! - also, again, you may include more than 2 Tables/Figures.)
NOTE: It is NOT necessary (or
even desirable) to use the Word or LATEX "templates"
provided. We want you to spend time on content, not formatting!!
5.
Papers must be submitted both electronically (to
6.
Supplemental information may be provided online. Include
the URLs in your manuscript.
To assist you in
ideas for projects and scope, here are the titles of projects from students in
this class over the last two years:
Comparison of
approaches for determining phylogenetic relationships (in turtles &
salamanders), including evaluation of high performance computing
mechanisms
Phylogenetic
relationships among Rec A gene family members, esp.
in maize
Identification of
genetic differences that determine ability of Campylobacter strains to colonize
turkey intestine
Identification
of genes that restore complement-resistance in attenuated Leishmania
strains
Microarray &
functional genomics analyses of phenol-induced proteins in Pseudomonas
Proteomic & functional/structural
genomics analyses of proteins expressed in developing retina
Bioinformatic analyses
of Lipcalin 2: structure, function, phylogeny
‘Adaptive
Thresholding’ Technique for Exon
Prediction
Genome-wide searching for the
tandem/inverted duplicated genes
in Arabidopsis
Sequence-based
Prediction of Protein-Ligand Interactions
Localized Tertiary
Protein Structure Prediction
Investigation
into the use of RNAi to prevent HIV infection