WELCOME: This course is 3 semester hours. The class meets for 2 hours of lecture each week. Course includes theory of computational methods to biological data analysis for discovery including Genomics, Proteomics, Transcriptomics. There will be two noncumulative exams for the first and the second part of the course. Context will include any material covered during lectures. Students will be required to complete an independent project upon completion of the course at the end of the term and present it to the class.
Course Prerequisites and Corequisites: Prerequisites graduate standing and permission of instructor, there is no corequisites.
Program Learning Outcomes:
Program Learning Outcome #1: The student will demonstrate a good knowledge base in biological concepts and be able to integrate knowledge with critical thinking skills to become problem solvers. Knowledge base will include: levels of complexity (molecular/cellular through population/communities/ecosystems), biological principles and processes.
Program Learning Outcome #2: The student will clearly communicate scientific information; provide clear structure and transitions, incorporating substantial primary-literature-based supporting evidence; and demonstrate audience appropriate purpose, agenda, language, and style.
Program Learning Outcome #3: The student will demonstrate an understanding of scientific methods and design small original scientific research project.
General Education Core Curriculum Objectives/Outcomes:
This course is not included in the general education core curriculum.
Student Learning Outcomes:
Students who complete Advanced Bioinformatics will be able to:
1. Understand structure of databanks (GenBank, PDB) and retreive needed data for genomic and proteomic research (PLO 1).
2. Demonstrate proper usage of online tools to analyze retrieved data (PLO 1,2).
3. Discuss the contributions of bioinformatics to research efforts in their field of study (PLO 1, 2).

ATTENDANCE: You are expected to attend all lectures according to the schedule– attendance will be monitored. Sign in with your full first name and last name as listed on the class roster. Students who do not provide their full name will be marked as absent. Missing lecture classes without university approved absences will result in points subtraction from your Final grade. In contrast perfect attendance will give you extra points to your Final grade. Stay focused: turn off your cellphone and pack it away, be respectful to your classmates and the professor. Using a phone during the class without permission will be equal to an absence. Missing an exam will be permitted only by prior arrangement. If the exam was missed without prior arrangement as an after the fact make-up will be allowed only by Faculty Notification Requests. (The information is located on the Dean of Student’s website: https://www.sfasu.edu/thehub/sos/notification-request )
CLASS DISRUPTION: Class disruptions will not be tolerated because they detract from other students’ learning. As adults, students should be able to sit through class without disturbing others.
The professor does NOT necessarily give you a warning or make an announcement that you are disrupting class. Instead, points will simply be deducted in the grade book. Students are free to inquire at any time whether they have had points deducted during office hours.
Tardiness to lecture will not be tolerated; it disrupts the lesson and the concentration of fellow students. Reasonable accommodations will be made in cases of emergency situations if documentation is provided. It is the student’s responsibility to provide the instructor with documentation of emergencies. Sleeping during class can be distracting to other students and the instructor. If a student is so tired that they cannot stay awake for a lecture, as boring as it may be, the student should not be in class. Cell phones must be turned off during lecture and packed away. In cases of family emergency the student must inform the instructor of the situation BEFORE class begins. There should be no texting in class. Texting may distract other students and the instructor. Leaving class is disruptive to other students who are trying to pay attention. Leaving the class for any reason will count against you. Hence, be sure to use the restroom before coming to class (a 5 minute break is given during lecture during the long summer lectures). If a student knows they will need to leave class early, notify the instructor well ahead of time. Points will not be deducted if the student has a legitimate excuse for leaving early. Talking/Disruptive Behaviors: the professor is highly encourages students to ask questions or make relevant comments during a lecture. However, talking to a neighbor or other disruptive behaviors will not be tolerated because, again, it disrupts the learning environment of other students. Laptop computers are not allowed in lecture. In the past, too many students have used them for surfing the internet or working on other projects during lecture, which distracts other students.
MATERIALS: Students will work with the information/instructions provided online. PowerPoint presentations for each lecture will be online, according to the provided schedule of the course. Handmade notes can be made and used during the exam. (REMEMBER: draw it to know it!) I recommend to use CHROMIUM to browse this page. Textbook is optional for this course: Concepts in Bioinformatics and Genomics, by Jamil Momand et al.
Two Exams (all together) - 80 pts
Quizzes/independent activities – 20 pts
Independent project for grad. students - 50 pts
TOTAL - 150 pts
M 19:00-20:00, T 12:30-16:30, or by appointment @S236
week meeting schedule topic activities lecture slides lecture video
History of Bioinformatics
Students presentations
Macromolecules for databases
Sequence databases
Molecular evolution
Sequence alignment and BLAST
MidTerm Exam
October 10 @4:00PM @D2L
Protein structure prediction.
Please discuss and critique your finding from last week assignment and make it better.
Independent project presentation abstracts are due Phylogenetics
Thanksgiving 🦃
Virtual Reality, drug design
Working on independent project
Final Exam
December 11 @4:00PM @D2L
Keck conference, Rice University https://arc2023.blogs.rice.edu
Keck seminar series, GCC, Rice University https://www.gulfcoastconsortia.org/home/training/keck-seminar/
Antimicrobial resistance program, GCC, Rice University https://www.gulfcoastconsortia.org/home/training/tpamr/
Communication with the professor is over an e-mail avankley@sfasu.edu (please DO NOT email through D2L ).

E-mail rules:
When emailing use your OFFICIAL SFA E-MAIL ADDRESS
Check your e-mail REGULARY and, if you have your SFA account forwarded to some secondary account, to be certain this is not full and can receive messages.
Always indicate BOTH class & section # and your CID in a subject line.
When ATTACHING a file, filename should be “First_LastName.ext”, it must also include your name in the document itself.
Emails lacking any of the information listed above WILL BE IGNORED.
BE courteous: Begin your email with a greeting that addresses your instructor respectfully and professionally, such as "Dear Dr. Smith" or "Hi Dr. Jones."
E-mail should be considered a professional form of communication – you should use proper grammar and spelling.
CLOSE with your full name: After your message, end with a closing and signature, such as "Sincerely, Jane Doe" or "Thanks, John Doe.”
A RESPONSE may take time: I will try to get back quickly, but don’t expect a response within a few minutes. It can take up to 24 hours for an instructor to respond. If you need a response ON THE SAME DAY, your best option is to attend the office hours.
NO emails will be answered after 5 p.m. and/or during weekends or holidays.
NO GRADE DISCUSSION over an e-mail, only during one on one meetings. Grades cannot be discussed via e-mail at any time due to federal law. I will speak to you in person instead during my office hours. DO NOT involve a third-party who is not affiliated in an official capacity with SFASU (e.g., friend, roommate) in any matters pertaining to your enrollment in this course. Your instructor is legally prohibited from discussing most course/grade-related issues with third parties according to the Family Educational Rights and Privacy Act (FERPA) (20 U.S.C. § 1232g; 34 CFR Part 99).
1901 Raguet Street N, Miller Science Building, Room 101
Nacogdoches, TX 75962