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Sacan Bioinformatics Lab
Drexel University
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Bioinformatics

Course Information

  • Office Hours (Note different zoom link)
    • We will hold office hours during the times listed below. Some of these office hours have both in-person and on-zoom options. The in-person office hours will be held on Bossone 7th floor lobby and/or in Bossone702. The zoom room for office hour is (different than course zoom link) at: https://drexel.zoom.us/j/88998283984?pwd=Q0NaTUE2Y0xQSUM1ZUxwcW1YcnN0Zz09 (password: bmes)
    • If you sign on to zoom and don't see any of us, please email us at: bmes544staff@umich.edu . Sometimes Zoom signs us out without us noticing or we may be in the incorrect zoom room.
    • Here are the office hour times (The times may change through the quarter, any changes will be announced in the Discussion Group):
      • See the Announcements (which you also receive as emails) for any changes to these times.
      • Mondays 2pm-3pm: Ahmet Sacan – in-person & on-zoom. (Please email for in-person meeting. No appointments necessary to join on Zoom).
      • Thursdays 10am-11am: Ahmet Sacan – in-person & on-zoom. (Please email for in-person meeting. No appointments necessary to join on Zoom).
      • Teaching Assistant office hours times by appointment only. Please email bmes544staff@umich.edu to request a meeting.
  • Required Textbook:
    • [ZB] M. Zvelebil, J.O. Baum. Understanding Bioinformatics. Garland Science. (An ebook version is also available from the publisher and/or elsewhere).
    • Most of our weekly reading material is from this book. You are expected to own/rent/have a copy of this book throughout the course.
  • Recommended Resources:
    • P. A. Pevzner, Computational Molecular Biology: An Algorithmic Approach. MIT press.
    • Edda Klipp, et.al. Systems Biology: A Textbook. Wiley-Blackwell.
    • Amos Gilat. MATLAB: An Introduction with Applications. Wiley.
    • John M. Zelle. Python Programming: An Introduction to Computer Science. Franklin Beedle & Assoc.
    • Mark Lutz. Learning Python: Powerful Object-Oriented Programming. OReilly.
    • Example course projects from Bmes483/543
  • Reviewing Blackboard Quiz Results and Answers:
    • The answers to quizzes are made available after their duedates.
    • To review your answers and the correct answers: Click on the test –> begin –> view all attempts –> click on your score
  • Dropbox instructions:
    • If you do not already have a Dropbox account, sign up for a free account on dropbox.com. You may sign up using any email address (e.g., drexel or gmail). You can use the free “Basic Plan”, upgrading to a paid or trial account is not necessary.
    • Download and install Dropbox if you do not already have it installed on your computer.
    • When the Dropbox app opens for the first time, it asks “Choose how to sync your files”. Select Make files local.
    • Important: When the Dropbox app asks “Want to keep your PC backed up?”, select Not right now.
      • If you do want to have Dropbox backup your Desktop, Documents, Downloads, etc. folders, just remember that you will likely run out of Dropbox space quickly and then it will be your responsibility to clear out enough Dropbox space to allow your course files. Selecting “Not right now” avoids that problem.
    • Open your Dropbox folder and create a subfolder named named bmes544.FirstnameLastname.abc123 (replace “FirstnameLastname” with your own name (no spaces) and “abc123” with your own Drexel username). Use “bmes544” in the folder name even if you are registered for Bmes484 section.
    • Visit dropbox.com and confirm that the course folder is now present there. You will also see a link for sharing. Share that folder with: ahmetmsacan@gmail.com . Make sure to give Edit permissions.
    • You will use your Dropbox course folder for programming assignments. Please do not store study material in that folder.
    • You will NOT need to share individual assignments; they will already be accessible by us.
    • Create a subfolder in your Dropbox course folder for each programming assignment (We may run an automated script to create some/all of these subfolders for you).
    • You must work within these subfolders for each assignment. Your files will be synchronized as you work on them.
    • Unless explicitly stated, all assignments must be completed individually. For any group assignments, each member of the group must have a final copy of the assignment in their own Dropbox folder. These copies should be identical. We may arbitrarily use one of the group member's files for grading.
    • Your Dropbox course folder should not exceed 100MB in size. (Most students use less than 20MB). A grading penalty toward your programming assignment grade will be applied if you exceed this limit. We may check for Dropbox space usage weekly and a penalty may be applied each time.
  • Appropriate Use of Course Materials:
    • Some or all of the course materials may be the intellectual property of the course instructor, Drexel University, or others. Use of this intellectual property is governed by Drexel University policies, including the IT-1 policy found here: https://drexel.edu/it/about/policies/policies/01-Acceptable-Use/
    • Course materials (including recordings and assignments), may not be copied, reproduced, distributed or re-posted. Doing so may be considered a breach of this policy and will be investigated and addressed as possible academic dishonesty, among other potential violations. Improper use of such materials may also constitute a violation of the University's Code of Conduct found here: https://drexel.edu/cpo/policies/cpo-1/ and will be investigated as such.
 

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