Bioinformatics Algorithms will focus on the types of analyses, tools, and databases that are available and commonly used in Bioinformatics. The workshops will apply the lecture material in the analysis of real data.

Prequisites

Note that computer programming in Java, Perl, or C/C++ will be required for most of the workshop assignments. The undergraduate course (BIOL-530) requires both BIOL-330 (Bioinformatics) and BIOL-289 (Fundamatals of Bioinformatics Programming). The graduate course (BIOL-630) requires matriculation into a BS/MS or MS program.

Each week, two hours are dedicated to "lecture". When the course is delivered in an online format, we will use this is a slightly different way than usual. Before lecture, students must read over the slides and prepare at least three questions they have about the slides and material for the week. Questions must be submitted as a Word/Open Office/Libre Office/plain text document to the appropriate Assignment box by midnight before the lecture.

During the assigned day/time we will break the two hours into the following structure, with short breaks as necessary. To earn credit for lecture, students must attend the full period with cameras on.

• Discuss student questions
• Work through examples as a class
• Breakout group activities

As noted in the above schedule, there will be regular workshop assignments. There are eight workshop assignments, of which you must chose five which compose a total of 40 pts. If you do more than 40 pts worth, only the first 40 pts of grading will count toward your course grade. For example, if you do 34 points of workshops (workshop 1, 2 for 10 pts and one for 8), the final workshop will be capped at 6 points. Also note that each workshop is only available for particular workshop periods, as in the table below. To make a perfect fit, only one 10 point workshop should be attempted (6 pt, 3 x 8 pt, 10 pt = 40 pts). Nota bene: if you do the BLAST workshop for period 2, you must do the Enrichment analysis for period 3.

After the first workshop, all assignments must be completed in Perl, C/C++, or Java. No other languages will be accepted. Specific requirements for each workshop are outlined in the individual assignments.

Participation in a workshop requires attendance on time and for the full period. During this time, it is expected that you will ask question, work with each other on problem solving, and generally make progress on the workshops.

If you choose to do additional workshops, after completing the required five, you may earn up to five bonus points toward the final grade for one, and no more than one, additional workshop. You must email Dr. Osier well in advance (before the start of class in Week 14) if you are interested in pursuing a bonus workshop assignment. Bonus workshops are due on Wednesday, December 15th, by noon. Due to grading deadlines, bonus workshops will not be accepted late.

Each workshop is due by the start of the next Workshop after the last week of it's period. For example, Workshop 1 is due before Workshop in Week 3 (September 8th). All workshop assignments must be submitted to the appropriate MyCourses DropBox before the deadline. Note that Workshop 4 is due by the Wednesday of Week 14 at the normal workshop time, and the final workshop is due by the start of the normal workshop time on Wednesday, Dec 15th.

Late workshops: 10% of a given workshop grade will be for on-time submission. Workshops will have weekly deliverables which must be submitted on time. Late deliverables may not be submitted more than one week late, and then without points for submitting on-time. Due to grading deadlines, the final lab may be submitted late by no later than 5am on Thursday, Dec 16th.

Due to a quirk of myCourses, late quizzes will be penalized 0.2 points for each minute, or portion of a minute, submitted late, but never below 0. So a quiz submitted 2.5 minutes late will be penalized 0.6 points.

Note that the class may receive official communication in person in class, by email, or in the myCourses Discussion group(s). Any and all are considered official communication methods.

For the first offense, anyone caught plagiarizing or otherwise cheating will receive a 0 (zero) on the quiz/exam/workshop, and be referred to the Head of the School of Life Sciences. In the event of a second offense, the student will receive an "F" for the course. If you have any questions about whether or not something constitutes plagiarism and/or cheating, please ask the instructor in advance. Duplicate submissions will also receive a grade of 0 (zero) for a workshop. In the case of especially egregious first offenses, the instructor reserves the right to assign a grade of "F" for the course, as per RIT policy.

Note that your code must also be written by yourself. You are encouraged to work with each other through discussion groups, but must in the end write all code on your own. Sufficient evidence of plagiarism on a workshop will be treated the same as for plagiarism or cheating in any other part of the course. The workshops will be checked for cheating.

Links

Will be added as needed.

Copyright notice

The legal use of distributed material is strictly limited to course activities, and not activity outside the course. The use of copyright protected material outside the RIT course may be prohibited by law.

COVID-19 Syllabus Addendum