Bio-Bio-1 Study Program II

Bio-Bio-1 Bioinformatics Study Program – II

Duration
10 weeks (25-Nov-2011 To 03-Feb-2012)

Resource Personnel
Fokhruz Zaman (zamanmisl@gmail.com)
Zohirul Alam Tiemoon (tiemoon@gmail.com)
Saddam Hossain (saddam_raj@yahoo.com)
Farjana Khatun (farjanakhtn.09@gmail.com)

Books (for detail references)
  • Bioinformatics Primer: An Introductory Handbook for Bioinformatics Practitioners, by Bio-Bio-1 (development in progress)
  • Biological sequence analysis: Probabilistic models of proteins and nucleic acids, by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
  • Introduction to Bioinformatics, by Arthur M. Lesk
  • A Computer Scientist’s Guide to Cell Biology: A Travelogue from a Stranger in a Strange Land, by William W. Cohen.
  • An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner
  • Computational Molecular Biology: An Algorithmic Approach, by Pavel A. Pevzner
  • Computational Molecular Biology: An Introduction, by Simon Levin, Editor-in-Chief, WILEY SERIES IN MATHEMATICAL AND COMPUTATIONAL BIOLOGY
  • Bioinformatics for Dummies, by Jean-Michel Claverie, Cedric Notredame
  • Bioinformatics Programming Using Python, by Mitchell L Model
  • Biopython Tutorial and Cookbook, by Je Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy nski
  • Applied Statistics for Bioinformatics using R, by Wim P. Krijnen

Schedule and Topics
Time: Friday 5:00pm to 6:30pm
Venue: Sanskriti Bikash Kendra, 1/E/1, Paribag, Dhaka-1000. [Map]

We will try to cover the following topics as per the following schedule (Ms Farjana Khatun will act as the key resource for these main streams of discussion):

Date
Topic
Resource Person
25 November, 2011
Bio-Bio-1 Orientation
Mr Fokhruz Zaman & Mr
Saddam Hossain
09 December, 2011
Introduction to Bioinformatics
Ms Farjana Khatun
16 December, 2011
DNA Sequencing - Reading the Blueprint of Life
Ms Farjana Khatun
23 December, 2011
Sequence Alignment
Ms Farjana Khatun
13 January, 2012
Gene prediction and Genome Analysis
Ms Farjana Khatun
20 January, 2012
Comparative Phylogeny and Tree Analysis
Ms Farjana Khatun
27 January, 2012
Structural Bioinformatics
Ms Farjana Khatun











Announcements
  • [01-Dec-2011] Bio-Bio-1 study session will not be held on this Friday, 2 December, 2011.
  • [30-Nov-2011] Installation guide of Ubuntu and Python has been uploaded. Find it here.
  • [22 December, 2011] Bio-Bio-1 Study Session of 23 December will be held at BASIS, Level 5, BDBL Bhaban (building between T.K bhaban and Titas gas building), Karwan Bazar.

Bioinformatics Study Works
  • Participants should attend all the regular discussion sessions.
  • Respective Bio-Bio-1 Team-Member will anchor the discussion & present a 30-45 minutes lecture on the scheduled bioinformatics topic.
  • After Bio-Bio-1 teams presentation, participant (individually) should do a presentation on some previously specified and agreed topic (topic and schedule will be decided before-hand).
  • Each participant will do at least three presentations.
  • Each participant will be assigned to some specific study topics / problems / research materials / study materials exploring which they will learn bioinformatics in practice

Bioinformatics Development works
  • Each participant from Computational background needs to develop a small tool / application pertaining to his/her assigned study topic.
  • Each participant from Life-science background needs to develop demonstrable computational skill relating to his/her assigned study topic.

Bioinformatics Literature Survey Works
Each participant needs to survey in his/her assigned bioinformatics topic in the literature and finally compile a survey documentation (at least 2-pages).

Bioinformatics Programming
Bioinfromatics programming skill using Python & R is must to have for each of the participant. Participants need to engage themselves willingly and inspired by own-self in the learning of Python & R. The need of programming skill for participants from Computational background and for participants from Life-Science background may differ, but every bioinformatician should have a minimal skill. (Mr Zohirul Alam Tiemoon will lead bioinformatics programming coaching)

Study Topics
Each participant has to dedicate some time and thought selecting his/her study topic first. First 3 weeks we will spend on it. We will suggest a list of topics (obviously topics will be of very specific and narrow scope) and discuss some aspects and over-views of those topics in the coming weeks. The list will grow in the coming weeks gradually. Participants may also suggest a study topic, but that must be verified by Bio-Bio-1.

Possible Topics
--possible topic, assigned participant, link to related resources : will be populated gradually (Mr Saddam Hossain will work as a mentor on this part)

  1. DNA Visualization or Graphical Representation of DNA
    1. [Md. Nafiul Alam Nion (CS)] DNA-Walk Model
    2. [Md. Rabiul Islam (CS)] z-Curve Model
    3. [?] Dual Vector Model
  2. Statistical Characterization of DNA sequences' Structural Elements
    1. [Tahashin (CS)] TATA-box & CAAT-Box
    2. [Santonu Kumar Sanyal (BS)] Study of CpG islands
    3. [S. M. Sabbir Alam (BS)] GC-contents, AT-contents, & GC-skewness, AT-skewness
  3. [Farjana Khatun (BS)] Bioinformatics Data Mining using WEKA (Tool orientation & survey)
  4. [Md. Aminul Islam Amin (CS)] A survey & review on BLAST (survey on tools, algorithms & applications)
  5. [Md. Anwar Siddique Raju (BS)] A survey & review on Multiple Sequence Alignment (MSA) - (survey on tools, algorithms & applications)
  6. [Polash Laskar (CS)] A Study on Application of Python & Bio-Python in Bioinformatics (survey on tools, features & applications)
  7. [Arafat Rahman (BS)] A survey & review on R & Bioconductor for Bioinformatics (survey on tools, features & applications)
  8. [?] A survey on Galaxy (survey on tools, features & applications, Modeling a Bioinformatics Problem)
  9. [Mohammad Arif Ashraf (BS)] HapMap Project
  10. [M. Sadman Sakib (BS)] Gene Clustering using Micro Array Expression Data
  11. [Md. Tarikul Islam (BS)] Protein Folding - Concepts, Algorithms, Applications
  12. [?] Haplotype Bioinformatics
  13. [Somen Kumar Mistri (BS)] Study on Phylogenetic Network
  14. [?] Phylogenetic Tree Reconstruction - Concepts, Algorithms, Techniques, Applications
  15. [?] Motifs Finding - different algorithms & tools
  16. [?] Clustering in bioinformatics - algorithms and applications
  17. [Md. Mirazul Islam (BS)] What is System Biology
  18. [?] A survey on Bioinformatics Software
  19. [?] A survey on Bioinformatics Databases
  20. [?] A survey on AI-algorithms in Bioinformatics
  21. [?] Bioinformatics Data mining
  22. [?] DNA computing - a new era of computation
  23. [Md. Nafiul Alam Nion (CS] HMM & Its application in Bioinformatics
  24. [Imran (BS)] Bioinformatics Business (/ Intellectual Property) Strategy - Industrialization and Commercialization of Bioinformatics : Bangladesh Perspective


Guidelines for Presentation

Guideline for tool / application development

Guidelines for Survey Documentation

Evaluation
Participants' performance will be evaluated on every point of this program. (Mr Fokhruz Zaman will lead this evaluation process)


Requirements
  • Linux OS (Ubuntu is suggested) should be installed in the participant’s work station.
  • Participants should learn themselves Python & R to the needed level of excellence. (Mr Zohirul Alam Tiemoon will help and direct on this part )


Web resources