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BME110, Spring 2012, Section 01: Syllabus
BME 110 / BIOL 181: Computational Biology Tools
This is a hands-on laboratory, lecture, & problem solving course geared to teach basic tools used in computational biology. Some topics covered include motif searching, sequence searches, multiple sequence alignment, genefinders, using genome annotation, phylogenetics, human SNP analysis, and viewing molecular structures from X-ray crystallography data. Web-based tools and databases are primarily used, but a few Java-based apps are also used. Open to all bioinformatics, bioengineering, or science students with basic biochemistry (or permission of the instructor).
You must bring your own laptop to class every day, and to discussion sections.
Instructor Office Hours:
Mon 1-2pm, Wed 11-Noon
Brandon Rice (firstname.lastname@example.org)
TA Office Hours:
Paola: Monday: 9:30am-10:30 Basking Lounge; Thursday: Noon-1pm PSB-213
Brandon: Tues and Thurs at 4pm-5pm, PSB 213
Discussion Sections (Required)
Genomes, Browsers, & Databases (2008) by Peter Schattner
There will also be numerous readings taken from scientific literature, on-line tutorials, and current news articles dealing with the rapidly changing social impact of genome information on our society.
Problem Sets: 25%
Final Exam: 30%
On-line Exercises, participation and attendance at lab sections: 20%
(One discussion section absence may be allowed if cleared with me ahead of time.
Homework Turn-In & Late Policy:
Homeworks turned in after the deadline will have 5% deducted if turned in within 24 hours,
Turn in homework electronically using the eCommons dropbox.
You may work together sharing ideas and teaching each other how to solve problems on study section sequences (i.e, Sequence-A, Sequence-B, etc.), but you must do the analyses for homework sequences (i.e. Sequence-1, Sequence-2, etc.) on your own, described in your own words. You may not share/trade/lend/borrow written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers with others (see below).
Academic Honesty and Academic Integrity:
In recent years, there has been an increased number of cheating incidents in many UC campuses, and unfortunately, UCSC is no exception. The School of Engineering has a zero tolerance policy for any incident of academic dishonesty. If cheating occurs, there may be consequences within the context of the course, and in addition, every case of academic dishonesty is referred to the students' college Provost, who then sets the disciplinary process in motion. Cheating in any part of the course may lead to failing the course and suspension or dismissal from the university.
What is cheating? In short, it is presenting someone else's work as your own. Examples would include copying another student's written or electronic homework assignment, or allowing your own work to be copied. Although you may discuss problems with fellow students, your collaboration must be at the level of ideas only. Legitimate collaboration ends when you "lend", "borrow", or "trade" written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers. If you do collaborate (legitimately) or receive help from anyone, you must credit them by placing their name(s) at the top of your paper.
What is Academic Integrity? This question is better answered with how we violate academic integrity. One prime example is fabrication. Fabrication:
Another example of violating academic integrity is Facilitating Academic Dishonesty:
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