Difference between revisions of "Syllabus"
 
Line 1: Line 1:
−
<h1 id="isc-5317-isc4933-undergraduate-section-graduate-course-computational-evolutionary-biology" class="unnumbered">ISC-5317 (+ISC4933 undergraduate section):<br />
+
<h1 class="unnumbered"
−
Graduate course: Computational Evolutionary Biology</h1>
+
id="graduateundergraduate-course-computational-evolutionary-biology">
−
<h2 id="class-meeting" class="unnumbered">Class Meeting</h2>
+
<strong>Graduate/Undergraduate course:<br />
 +
Computational Evolutionary Biology</strong></h1>
 +
<h2 class="unnumbered" id="class-meeting">Class Meeting</h2>
 
<p>Lectures:<br />
 
<p>Lectures:<br />
−
Tuesdays and Thursdays 2:00-3:15 PM Dirac Science Library Room 152</p>
+
Tuesdays and Thursdays 1:20-2:35 PM Dirac Science Library Room 422</p>
−
<h2 id="instructor" class="unnumbered">Instructor</h2>
+
<h2 class="unnumbered" id="instructor">Instructor</h2>
 
<p>Peter Beerli<br />
 
<p>Peter Beerli<br />
 
Office: 150-T DSL<br />
 
Office: 150-T DSL<br />
 
Email: beerli@fsu.edu<br />
 
Email: beerli@fsu.edu<br />
−
Phone: (850) 559-9664</p>
+
Cell: (850) 559-9664 [Text appreciated]</p>
−
<!-- <h2 id="class-assistant" class="unnumbered">Class Assistant</h2>
+
<h2 class="unnumbered" id="office-hours">Office Hours</h2>
−
<p>Marjan Sadeghi<br />
+
<p>Monday usually 1:00-3:00 PM by appointment.</p>
−
Office: 150-J DSL<br />
+
<h2 class="unnumbered" id="objectives">Objectives</h2>
−
Email: ms16ac@my.fsu.edu</p> -->
+
<p>This course will introduce students to methods used in phylogenetics
−
<h2 id="office-hours" class="unnumbered">Office Hours</h2>
+
and population genetics and writing computer programs using these
 +
methods. The primary objectives of the course are:</p>
 +
<ol>
 +
<li><p>to expose students to a large set of modern methods used in
 +
theoretical evolutionary biology and learn about the details of often
 +
used methods in phylogenetic and population genetics analyses.</p></li>
 +
<li><p>to introduce students to the programming aspects of the field.
 +
Students will learn and use the programming language Python to develop
 +
scripts and to understand the details of the methods. Learning Python
 +
will be assisted using AI technology (chatGPT) which we will use
 +
extensively to write code.</p></li>
 +
<li><p>to empower students to develop programming and analysis skills
 +
that involve the development of scripts to change data format, execute
 +
applications, and analyze results.</p></li>
 +
</ol>
 +
<h2 class="unnumbered" id="rational-for-the-objectives">Rational for the
 +
objectives</h2>
 +
<p>Current biological studies have started to emphasize the importance
 +
of data analytics, but still, most courses simply use packaged programs,
 +
leaving the students at a disadvantage if no courses exist that improve
 +
the computational skills of students. This course prepares students for
 +
such a challenge.</p>
 +
<h2 class="unnumbered" id="content">Content</h2>
 +
<p>Advanced computational methods are becoming increasingly important in
 +
biology. A wide range of applications — including, for instance,
 +
identifying pathogens, tracing viral transmission pathways, and
 +
reconstructing the geographic expansion of humans out of Africa — rely
 +
on evolutionary inference. This course will cover the methods currently
 +
used for evolutionary inference, the stochastic models and inference
 +
principles they are based on, and how they are implemented in practice.
 +
The students will get hands-on experience in developing computational
 +
software. We expect that the students leave the course with the
 +
necessary skills to develop their own ideas and develop projects based
 +
on simulated data sets and scripts.</p>
 +
<h2 class="unnumbered" id="textbook">Textbook</h2>
 +
<p>We do not use a textbook, but if you feel that you need a book use
 +
this one: Yang, Z. 2006. Computational Molecular Evolution. Oxford
 +
University Press, Oxford, England. (Book website:
 +
http://abacus.gene.ucl.ac.uk/CME/)</p>
 +
<h2 class="unnumbered" id="grading">Grading</h2>
 
<ul>
 
<ul>
−
<li><p>Peter Beerli: by appointment (email: beerli@fsu.edu); or just come to my office, If do not have a meeting I will have time for you.</p></li>
+
<li><p>Grades will be based on students’ execution of programming
 +
assignments, each of which involves understanding the algorithms, code
 +
design, and program documentation [10 points each]</p></li>
 +
<li><p>Each student will work on a project on their own during the last
 +
4 weeks of the semester and also give a short presentation of their work
 +
in the last regular lab-meeting. [15 points for the report and 15 points
 +
for the presentation]</p></li>
 +
<li><p>I take the liberty to quiz you about your assignments if I get
 +
the impression that you let chatGPT do all the work and you do not
 +
understand what is happening in your own code. Using a tool like chatGPT
 +
does not absolve you from learning the tools/methods. The quiz will
 +
affect the grade for the assignment either positively or
 +
negatively.</p></li>
 +
<li><p>There will be no mid-term and final exams; the project
 +
substitutes for a final examination.</p></li>
 
</ul>
 
</ul>
−
<h2 id="objectives" class="unnumbered">Objectives</h2>
+
<p>A student who accumulates 90% or more of the possible points will
−
<p>This course will introduce students to methods used in phylogenetics and population genetics and writing computer programs using such methods. Primary objectives of the course are:</p>
+
receive a grade of "A", a student who accumulates between 80% and 89% of
 +
the possible points will receive a grade of "B", a student who
 +
accumulates between 70% and 79% of the possible points will receive a
 +
grade of "C", a student who accumulates between 60% and 69% of the
 +
possible points will receive a grade of "D", and a student who
 +
accumulates less than 60% of the possible points will receive a grade of
 +
"F".</p>
 +
<h2 class="unnumbered" id="missedlate-assignments">Missed/Late
 +
Assignments</h2>
 +
<p>Deadlines for assignments will be announced in class; late
 +
assignments will be accepted for full grade only in meidcal cases. 10%
 +
of the points are deducted per day for late assignments; An assignment 1
 +
day late will be 90% of the points, 2 days late 80%, ... If you think
 +
that the assignments are too difficult and you cannot get it right even
 +
with the help of chatGPT, talk to me early, I will not have time on the
 +
evening of the due date.</p>
 +
<h2 class="unnumbered" id="university-attendance-policy">University
 +
Attendance Policy:</h2>
 +
<p>Excused absences include documented illness, deaths in the family,
 +
and other documented crises, call to active military duty or jury duty,
 +
religious holy days, and official University activities. These absences
 +
will be accommodated in a way that does not arbitrarily penalize
 +
students who have a valid written excuse. Consideration will also be
 +
given to students whose dependent children experience serious
 +
illness.</p>
 +
<h2 class="unnumbered" id="academic-honor-policy">Academic Honor
 +
Policy:</h2>
 +
<p>The Florida State University Academic Honor Policy outlines the
 +
University’s expectations for the integrity of student’s academic work,
 +
the procedures for resolving alleged violations of those expectations,
 +
and the rights and responsibilities of students and faculty members
 +
throughout the process. Students are responsible for reading the
 +
Academic Honor Policy and for living up to their pledge to “. . . be
 +
honest and truthful and . . . [to] strive for personal and institutional
 +
integrity at Florida State University.” (Florida State University
 +
Academic Honor Policy, found at
 +
http://fda.fsu.edu/academic-resources/academic-integrity-and-grievances/academic-honor-policy)</p>
 +
<h2 class="unnumbered" id="americans-with-disabilities-act">Americans
 +
With Disabilities Act:</h2>
 +
<p>Florida State University (FSU) values diversity and inclusion; we are
 +
committed to a climate of mutual respect and full participation. Our
 +
goal is to create learning environments that are usable, equitable,
 +
inclusive, and welcoming. FSU is committed to providing reasonable
 +
accommodation for all persons with disabilities in a manner that is
 +
consistent with the academic standards of the course while empowering
 +
the student to meet the integral requirements of the course. Students
 +
with disabilities needing academic accommodation should: (1) register
 +
with and provide documentation to the Office of Accessibility Services;
 +
and (2) request a letter from the Office of Accessibility Services to be
 +
sent to the instructor indicating the need for accommodation and what
 +
type; and (3) meet (in person, via phone, email, skype, zoom, etc...)
 +
with each instructor to whom a letter of accommodation was sent to
 +
review approved accommodations. Please note that instructors are not
 +
allowed to provide classroom accommodations to a student until
 +
appropriate verification from the Office of Accessibility Services has
 +
been provided. This syllabus and other class materials are available in
 +
an alternative format upon request. For the latest version of this
 +
statement and more information about services available to FSU students
 +
with disabilities, contact the:</p>
 +
<p>Office of Accessibility Services<br />
 +
874 Traditions Way<br />
 +
108 Student Services Building<br />
 +
Florida State University<br />
 +
Tallahassee, FL 32306-4167<br />
 +
(850) 644-9566 (voice)<br />
 +
(850) 644-8504 (TDD)<br />
 +
oas@fsu.edu<br />
 +
https://dsst.fsu.edu/oas<br />
 +
</p>
 +
<h2 class="unnumbered" id="academic-success">Academic Success:</h2>
 +
<p>Your academic success is a top priority for Florida State University.
 +
University resources to help you succeed include tutoring centers,
 +
computer labs, counseling and health services, and services for
 +
designated groups, such as veterans and students with disabilities. The
 +
following information is not exhaustive, so please check with your
 +
advisor or the Department of Student Support and Transitions to learn
 +
more.</p>
 +
<h2 class="unnumbered" id="confidential-campus-resources">CONFIDENTIAL
 +
CAMPUS RESOURCES:</h2>
 +
<p>centers and programs are available to assist students with navigating
 +
stressors that might impact academic success. These include the
 +
following:</p>
 +
<p>Victim Advocate Program<br />
 +
University Center A, Rm. 4100<br />
 +
(850) 644-7161<br />
 +
Available 24/7/365<br />
 +
Office Hours: M-F 8-5<br />
 +
https://dsst.fsu.edu/vap<br />
 +
</p>
 +
<h2 class="unnumbered"
 +
id="counseling-and-psychological-services-caps">Counseling and
 +
Psychological Services (CAPS)</h2>
 +
<p>Florida State University’s Counseling and Psychological Services
 +
(CAPS) primary mission is to address psychological needs and personal
 +
concerns, which may interfere with students’ academic progress, social
 +
development, and emotional well-being. The following in-person and
 +
virtual (tele-mental health) services are available to all enrolled
 +
students residing in the state of Florida:</p>
 
<ol>
 
<ol>
−
<li><p>to expose students to a large set of modern methods used in the field of theoretical evolutionary biology, and learn about the details of often used methods in phylogenetic analysis and population genetics analysis.</p></li>
+
<li><p>Individual therapy</p></li>
−
<li><p>to introduce students to the programming aspects of the field. Students will learn and use the programming language Python to develop scripts and to understand details of the methods.</p></li>
+
<li><p>Group therapy</p></li>
−
<li><p>to empower students to develop programming and analysis skills that involve development of scripts to change data format, execute applications, and analyze results.</p></li>
+
<li><p>Crisis Intervention</p></li>
 +
<li><p>Psychoeducational and outreach programming</p></li>
 +
<li><p>After hours crisis-hotline</p></li>
 +
<li><p>Access to community providers for specialized treatment</p></li>
 
</ol>
 
</ol>
−
<h2 id="content" class="unnumbered">Content</h2>
+
<p>Call 850-644-TALK (8255) for more information on how to initiate
−
<p>Advanced computational methods are becoming increasingly important in biology. A wide range of applications — including, for instance, identifying pathogens, tracing viral transmission pathways, and reconstructing the geographic expansion of humans out of Africa — rely on evolutionary inference. This course will cover the methods currently used for evolutionary inference, the stochastic models and inference principles they are based on, and how they are implemented in practice. The students will get hands-on experience in developing computational software implementing these methods. We expect that the students leave the course with the necessary skills to develop their own ideas and are able to develop projects that are based on simulated data sets and scripts.</p>
+
services.</p>
−
<h2 id="textbook" class="unnumbered">Textbook</h2>
+
<p>Counseling and Psychological Services<br />
−
<p>We will have no textbook, but we have extensive handouts available through the course website.</p>
+
250 Askew Student Life Center<br />
−
<h2 id="grading" class="unnumbered">Grading</h2>
+
942 Learning Way<br />
−
<ul>
+
(850) 644-TALK (8255)<br />
−
<li><p>Grades will be based on students’ execution of the 7 assignments. Programming assignment will be judged on understanding the algorithms, code design, and program documentation. Summaries will be judged on being concise and accurate. [100 points each]</p></li>
+
Walk-in and Appointment Hours:<br />
−
<li><p>Either two students or a single student will work on a project on their own during the last few weeks of the semester and give a short presentation of their work during the last two classes periods. I expect that group projects are twice as large as single student projects [100 points for the report and 100 points for the presentation]</p></li>
+
M-F 8 am – 4 pm<br />
−
<li><p>There will be no midterm and no final exam, the project substitutes for a final examination. The total number of points is 900.</p></li>
+
https://counseling.fsu.edu/<br />
−
</ul>
+
</p>
−
<p><span><strong>A graduate student</strong></span> who accumulates 90% or more of the possible 900 points will receive a grade of "A", a student who accumulates between 80% and 89% of the possible points will receive a grade of "B", a student who accumulates between 70% and 79% of the possible points will receive a grade of "C", a student who accumulates between 60% and 69% of the possible points will receive a grade of "D", and a student who accumulates less than 60% of the possible points will receive a grade of "F".</p>
+
<h2 class="unnumbered"
−
<p><span><strong>An undergraduate student</strong></span> who accumulates 80% or more of the possible 900 points will receive a grade of "A", a student who accumulates between 70% and 79% of the possible points will receive a grade of "B", a student who accumulates between 60 % and 69% of the possible points will receive a grade of "C", a student who accumulates between 50% and 59% of the possible points will receive a grade of "D", and a student who accumulates less than 50% of the possible points will receive a grade of "F".</p>
+
id="services-at-uhs-are-available-to-all-enrolled-students-residing-in-florida">Services
−
<h2 id="missedlate-assignments" class="unnumbered">Missed/Late Assignments</h2>
+
at UHS are available to all enrolled students residing in Florida:</h2>
−
<p>Deadlines for assignments will be announced in class, when no deadline is given then the deadline is automatically 7 days later, deadline is usually 11:59pm; late assignments will be accepted for full grade only under extreme and documented circumstances. 5% of the total points (100pt) are deducted per day for late assignments.</p>
+
<p>The mission of University Health Services (UHS) is to promote and
−
<h2 id="university-attendance-policy" class="unnumbered">University Attendance Policy</h2>
+
improve the overall health and well-being of FSU students. UHS provides
−
<p>Excused absences include documented illness, deaths in the family and other documented crises, call to active military duty or jury duty, religious holy days, and official University activities. These absences will be accommodated in a way that does not arbitrarily penalize students who have a valid excuse. Consideration will also be given to students whose dependent children experience serious illness.</p>
+
a coordinated continuum of care through prevention, intervention, and
−
<h2 id="academic-honor-policy" class="unnumbered">Academic Honor Policy</h2>
+
treatment. Services include general medical care, priority care,
−
<p>The Florida State University Academic Honor Policy outlines the University’s expectations for the integrity of students’ academic work, the procedures for resolving alleged violations of those expectations, and the rights and responsibilities of students and faculty members throughout the process. Students are responsible for reading the Academic Honor Policy and for living up to their pledge to “. . . be honest and truthful and ... [to] strive for personal and institutional integrity at Florida State University." (Florida State University Academic Honor Policy, found at http://dof.fsu.edu/honorpolicy.htm.)</p>
+
gynecological services, physicals, allergy injection clinic,
−
<h2 id="americans-with-disabilities-act" class="unnumbered">Americans With Disabilities Act</h2>
+
immunizations, diagnostic imaging, physical therapy, and a medical
−
<p>Students with disabilities needing academic accommodation should: (1) register with and provide documentation to the Student Disability Resource Center; and (2) bring a letter to the instructor indicating the need for accommodation and what type. Please note that instructors are not allowed to provide classroom accommodation to a student until appropriate verification from the Student Disability Resource Center has been provided. This syllabus and other class materials are available in alternative format upon request. For more information about services available to FSU students with disabilities, contact the:</p>
+
response unit. The Center for Health Advocacy and Wellness (CHAW)
−
<p>Student Disability Resource Center 874 Traditions Way 108, Student Services Building, Florida State University, Tallahassee, FL 32306-4167<br />
+
assists students in their academic success through individual, group,
−
voice: (850) 644-9566, TDD: (850) 644-8504<br />
+
and population-based health and wellness initiatives. Topics include
−
Email: sdrc@admin.fsu.edu ; Website: http://www.disabilitycenter.fsu.edu/</p>
+
wellness, alcohol and other drugs, hazing prevention, nutrition and body
−
<h2 id="free-tutoring-from-fsu" class="unnumbered">Free Tutoring from FSU</h2>
+
image, sexual health, and power based personal violence prevention. For
−
<p>For tutoring and writing help in any course at Florida State University, visit the Academic Center for Excellence (ACE) Tutoring Services’ comprehensive list of tutoring options - see http://ace.fsu.edu/tutoring or contact tutor@fsu.edu for more information. High-quality tutoring is available by appointment and on a walk-in basis. These services are offered by tutors trained to encourage the highest level of individual academic success while upholding personal academic integrity.</p>
+
more information, go to uhs.fsu.edu.</p>
−
<h2 id="syllabus-change-policy" class="unnumbered">Syllabus Change Policy</h2>
+
<p>University Health Services<br />
−
<p>Except for changes that substantially affect implementation of the evaluation (grading) statement, this syllabus is a guide for the course and is subject to change with advance notice.</p>
+
Health and Wellness Center<br />
−
<h2 id="lectures-topic-overview" class="unnumbered">Lectures: Topic overview</h2>
+
960 Learning Way<br />
 +
Tallahassee, FL 32306<br />
 +
Hours: M-F, 8 am– 4 pm<br />
 +
(850) 644-6230<br />
 +
https://uhs.fsu.edu/<br />
 +
</p>
 +
<h2 class="unnumbered" id="free-tutoring-from-fsu">Free Tutoring from
 +
FSU</h2>
 +
<p>On-campus tutoring and writing assistance are available for many
 +
courses at Florida State University. For more information, visit the
 +
Academic Center for Excellence (ACE) Tutoring Services, for a
 +
comprehensive list of on-campus tutoring options, see
 +
https://ace.fsu.edu/tutoring or contact tutor@fsu.edu. High-quality
 +
tutoring is available by appointment and on a walk-in basis. These
 +
services are offered by tutors trained to encourage the highest level of
 +
individual academic success while upholding personal academic
 +
integrity.</p>
 +
<h2 class="unnumbered" id="syllabus-change-policy">Syllabus Change
 +
Policy</h2>
 +
<p>Except for changes that substantially affect the implementation of
 +
the evaluation (grading) statement, this syllabus is a guide for the
 +
course and is subject to change with advance notice.</p>
 +
<h2 class="unnumbered"
 +
id="statement-on-public-health-protocols">Statement on Public Health
 +
Protocols</h2>
 +
<p>Class meets in person. If necessary, however, we will shift to remote
 +
instruction. There are currently no mask mandates in place at FSU, but
 +
if you feel more secure wearing a mask do so. If you feel sick please
 +
let me know by email and stay home. You can find up-to-date guidance at:
 +
https://stayhealthy.fsu.edu.</p>
 +
<h2 class="unnumbered" id="lectures-topic-overview">Lectures: Topic
 +
overview</h2>
 +
<p>Course material will be on CANVAS and also on my own website
 +
https://peterbeerli.com (classes)</p>
 
<ol>
 
<ol>
 
<li><p>Processes and patterns</p>
 
<li><p>Processes and patterns</p>
 
<ul>
 
<ul>
−
<li><p>Population genetics: Wright-Fisher population models, coalescence theory;</p></li>
+
<li><p>Population genetics: Wright-Fisher population models, Moran
−
<li><p>Phylogenetics: tree structures, speciation, Gene tree versus Species tree</p></li>
+
model, coalescence theory, genetic drift, gene flow, selection;</p></li>
−
<li><p>Mutation models: mutation/substitution model</p></li>
+
<li><p>Phylogenetics: tree structures, speciation, birth/death models,
 +
Gene tree versus Species tree</p></li>
 +
<li><p>Mutation models: real data (microsatellite markers, SNPs,
 +
sequences), modeling data, mutation/substitution model</p></li>
 
<li><p>Simulation of data</p></li>
 
<li><p>Simulation of data</p></li>
 
</ul></li>
 
</ul></li>
Line 63: Line 254:
 
<ul>
 
<ul>
 
<li><p>Parsimony and Distance methods</p></li>
 
<li><p>Parsimony and Distance methods</p></li>
−
<li><p>Maximum likelihood, Bayesian inference, Monte Carlo, Markov chain Monte Carlo,</p></li>
+
<li><p>Maximum likelihood, Bayesian inference, Markov chain Monte
 +
Carlo,</p></li>
 +
<li><p>Approximate Bayesian Computation</p></li>
 
<li><p>Model selection</p></li>
 
<li><p>Model selection</p></li>
 
<li><p>Bootstrap/Jacknife</p></li>
 
<li><p>Bootstrap/Jacknife</p></li>
 
</ul></li>
 
</ul></li>
 
</ol>
 
</ol>
−
<p>Each topic will include computational algorithms, problematic aspects such as convergence, biases, main focus will be on Bayesian and maximum likelihood methods.</p>
+
<p>Each topic will include computational algorithms, problematic aspects
−
<h2 id="assignments" class="unnumbered">Assignments</h2>
+
such as convergence, biases, main focus will be on Bayesian and maximum
−
<p>This list of assignments is an example, difficulty of assignments will depend on the overall class programming skills. Each assignment topic will be introduced in detail during class. The final set of assignments is not specified yet but it will look similar/same to the ones shown below:</p>
+
likelihood methods.</p>
−
<ol>
+
<h2 class="unnumbered"
−
<li><p>Assignment 1: print the most parsimonous tree using PAUP*</p></li>
+
id="homeworkassignments">Homework/Assignments</h2>
−
<li><p>Assignment 2: write a python code to simulate the substitution process.</p></li>
+
<p>Homework assignment (each will be 10 points) follow the weekly
−
<li><p>Assignment 3: write a summary about maximum likelihood estimation on trees (not less than 180 word, not more than 250)</p></li>
+
outline and usually will be given on Thursdays, and expected to be
−
<li><p>Assignment 4: write a summary about Bayesian inference (not less than 180 word, not more than 250)</p></li>
+
turned in on next Thursday morning. The project consists of an outline
−
<li><p>Assignment 5: Genetic drift simulation in Python</p></li>
+
(10 points), a presentation (15 points) and a report (not more than 8
−
<li><p>Assignment 6: Migrate tutorial</p></li>
+
pages) (15 points).</p>
−
<li><p>Assignment 7: Describe your Project in 180 to 250 words</p></li>
+
<h2 class="unnumbered" id="lecture-schedule">Lecture Schedule</h2>
−
<li><p>Project: The project will discuss either (1) a complex analysis of data or (2) software development or (3) a theory section we did not discuss. The project consists of two parts, a report (of not more than 8 pages) and a presentation of 10 minutes. We will develop ideas for the project during class.</p></li>
+
<table>
−
</ol>
+
<thead>
−
<p>All assignments and projects will be submitted through CANVAS.</p>
+
<tr>
−
<h2 id="lecture-schedule" class="unnumbered">Lecture Schedule</h2>
+
<th style="text-align: center;">Week</th>
−
<ol>
+
<th style="text-align: left;">days</th>
−
<li><p>Introduction. Trees and tree representation (Aug. 27)</p></li>
+
<th style="text-align: left;">Topic</th>
−
<li><p>Python and trees [Self study: Python tutorial] (Aug. 29)</p></li>
+
<th style="text-align: left;">Practice</th>
−
<li><p>Selfstudy: Parsimony (Sep 3)</p></li>
+
</tr>
−
<li><p>Selfstudy: Install PAUP* [Assignment 1] (Sep 5)</p></li>
+
</thead>
−
<li><p>Number of trees; Searching for the best tree(s) (Sep 10)</p></li>
+
<tbody>
−
<li><p>Substitution models and distance measures(Sep 12)</p></li>
+
<tr>
−
<li><p>Substitution models exercise (Sep 17) [Assignment 2]</p></li>
+
<td style="text-align: center;">1</td>
−
<li><p>Paul Lewis: Maximum likelihood, substitution model and trees (Sep 19)</p></li>
+
<td style="text-align: left;">8/27,29</td>
−
<li><p>Paul Lewis: Tree likelihood and rate heterogeneity (Sep 24) [Assignment 3]</p></li>
+
<td style="text-align: left;">intro/tree</td>
−
<li><p>Paul Lewis: Bayesian inference and Markov Chain Monte Carlo (Sep 26)</p></li>
+
<td style="text-align: left;">chatgpt,writing and reading trees</td>
−
<li><p>Paul Lewis: Bayesian inference on Trees (Oct 1) [Assignment 4]</p></li>
+
</tr>
−
<li><p>Question and Answer session about Paul Lewis lecture (Oct 3)</p></li>
+
<tr>
−
<li><p>Population genetics introduction (Oct 8)</p></li>
+
<td style="text-align: center;">2</td>
−
<li><p>Population simulation in Python [Assignment 5] (Oct 10)</p></li>
+
<td style="text-align: left;">9/3,5</td>
−
<li><p>The coalescent (Oct 15)</p></li>
+
<td style="text-align: left;">optimality/tree search</td>
−
<li><p>Coalescent simulation and extensions to the coalescent (Oct 17)</p></li>
+
<td style="text-align: left;">counting trees</td>
−
<li><p>Coalescent simulation in Python [Assignment 6] (Oct 22)</p></li>
+
</tr>
−
<li><p>Gene tree vs Species tree (Oct 24)</p></li>
+
<tr>
−
<li><p>SVD quartets and other PAUP* evaluations (Oct 29)</p></li>
+
<td style="text-align: center;">3</td>
−
<li><p>Analysis of admixture, networks (Nov 5)</p></li>
+
<td style="text-align: left;">9/10,12</td>
−
<li><p>Model Selection (Nov 7) [Assignment 7]</p></li>
+
<td style="text-align: left;">parsimony (fitch, sankoff)</td>
−
<li><p>Model Selection exercise using Migrate (Nov 12)</p></li>
+
<td style="text-align: left;">impl. Fitch with chatgpt</td>
−
<li><p>Bootstrap/Jacknife with PAUP* (Nov 14 )</p></li>
+
</tr>
−
<li><p>Project (Nov 19)</p></li>
+
<tr>
−
<li><p>Project (Nov 21)</p></li>
+
<td style="text-align: center;">4</td>
−
<li><p>Project (Nov 26)</p></li>
+
<td style="text-align: left;">9/17,19</td>
−
<li><p>Thanksgiving break</p></li>
+
<td style="text-align: left;">mutation models</td>
−
<li><p>Presentation (Dec 3)</p></li>
+
<td style="text-align: left;">distance methods</td>
−
<li><p>Presentation (Dec 5)</p></li>
+
</tr>
−
</ol>
+
<tr>
−
<p><span>Peter Beerli, August 2019</span></p>
+
<td style="text-align: center;">5</td>
 +
<td style="text-align: left;">9/24,26</td>
 +
<td style="text-align: left;">mutation models</td>
 +
<td style="text-align: left;">(finite vs infinite sites models)</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">6</td>
 +
<td style="text-align: left;">10/1,3</td>
 +
<td style="text-align: left;">likelihood</td>
 +
<td style="text-align: left;">creating a likelihood program</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">7</td>
 +
<td style="text-align: left;">10/8,10</td>
 +
<td style="text-align: left;">rate heterogeneity</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">8</td>
 +
<td style="text-align: left;">10/15,17</td>
 +
<td style="text-align: left;">bootstrap/jacknive</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">9</td>
 +
<td style="text-align: left;">10/22,24</td>
 +
<td style="text-align: left;">Bayesian inference</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">10</td>
 +
<td style="text-align: left;">10/29,31</td>
 +
<td style="text-align: left;">Priors</td>
 +
<td style="text-align: left;">Approximate Bayes sampler</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">11</td>
 +
<td style="text-align: left;">11/5,7</td>
 +
<td style="text-align: left;">MCMC</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">12</td>
 +
<td style="text-align: left;">11/12,14</td>
 +
<td style="text-align: left;">Coalescence 1</td>
 +
<td style="text-align: left;">simulation of trees and sequences</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">13</td>
 +
<td style="text-align: left;">11/19,21</td>
 +
<td style="text-align: left;">Coalescence 2</td>
 +
<td style="text-align: left;">estimation of population size</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">14</td>
 +
<td style="text-align: left;">11/26</td>
 +
<td style="text-align: left;">Project time</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">15</td>
 +
<td style="text-align: left;">12/3,5</td>
 +
<td style="text-align: left;">Project time (presentation)</td>
 +
<td style="text-align: left;"></td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<p><span>Peter Beerli, August 2024</span></p>

Latest revision as of 17:09, 27 August 2024

Graduate/Undergraduate course:
Computational Evolutionary Biology

Class Meeting

Lectures:
Tuesdays and Thursdays 1:20-2:35 PM Dirac Science Library Room 422

Instructor

Peter Beerli
Office: 150-T DSL
Email: beerli@fsu.edu
Cell: (850) 559-9664 [Text appreciated]

Office Hours

Monday usually 1:00-3:00 PM by appointment.

Objectives

This course will introduce students to methods used in phylogenetics and population genetics and writing computer programs using these methods. The primary objectives of the course are:

  1. to expose students to a large set of modern methods used in theoretical evolutionary biology and learn about the details of often used methods in phylogenetic and population genetics analyses.

  2. to introduce students to the programming aspects of the field. Students will learn and use the programming language Python to develop scripts and to understand the details of the methods. Learning Python will be assisted using AI technology (chatGPT) which we will use extensively to write code.

  3. to empower students to develop programming and analysis skills that involve the development of scripts to change data format, execute applications, and analyze results.

Rational for the objectives

Current biological studies have started to emphasize the importance of data analytics, but still, most courses simply use packaged programs, leaving the students at a disadvantage if no courses exist that improve the computational skills of students. This course prepares students for such a challenge.

Content

Advanced computational methods are becoming increasingly important in biology. A wide range of applications — including, for instance, identifying pathogens, tracing viral transmission pathways, and reconstructing the geographic expansion of humans out of Africa — rely on evolutionary inference. This course will cover the methods currently used for evolutionary inference, the stochastic models and inference principles they are based on, and how they are implemented in practice. The students will get hands-on experience in developing computational software. We expect that the students leave the course with the necessary skills to develop their own ideas and develop projects based on simulated data sets and scripts.

Textbook

We do not use a textbook, but if you feel that you need a book use this one: Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, Oxford, England. (Book website: http://abacus.gene.ucl.ac.uk/CME/)

Grading

  • Grades will be based on students’ execution of programming assignments, each of which involves understanding the algorithms, code design, and program documentation [10 points each]

  • Each student will work on a project on their own during the last 4 weeks of the semester and also give a short presentation of their work in the last regular lab-meeting. [15 points for the report and 15 points for the presentation]

  • I take the liberty to quiz you about your assignments if I get the impression that you let chatGPT do all the work and you do not understand what is happening in your own code. Using a tool like chatGPT does not absolve you from learning the tools/methods. The quiz will affect the grade for the assignment either positively or negatively.

  • There will be no mid-term and final exams; the project substitutes for a final examination.

A student who accumulates 90% or more of the possible points will receive a grade of "A", a student who accumulates between 80% and 89% of the possible points will receive a grade of "B", a student who accumulates between 70% and 79% of the possible points will receive a grade of "C", a student who accumulates between 60% and 69% of the possible points will receive a grade of "D", and a student who accumulates less than 60% of the possible points will receive a grade of "F".

Missed/Late Assignments

Deadlines for assignments will be announced in class; late assignments will be accepted for full grade only in meidcal cases. 10% of the points are deducted per day for late assignments; An assignment 1 day late will be 90% of the points, 2 days late 80%, ... If you think that the assignments are too difficult and you cannot get it right even with the help of chatGPT, talk to me early, I will not have time on the evening of the due date.

University Attendance Policy:

Excused absences include documented illness, deaths in the family, and other documented crises, call to active military duty or jury duty, religious holy days, and official University activities. These absences will be accommodated in a way that does not arbitrarily penalize students who have a valid written excuse. Consideration will also be given to students whose dependent children experience serious illness.

Academic Honor Policy:

The Florida State University Academic Honor Policy outlines the University’s expectations for the integrity of student’s academic work, the procedures for resolving alleged violations of those expectations, and the rights and responsibilities of students and faculty members throughout the process. Students are responsible for reading the Academic Honor Policy and for living up to their pledge to “. . . be honest and truthful and . . . [to] strive for personal and institutional integrity at Florida State University.” (Florida State University Academic Honor Policy, found at http://fda.fsu.edu/academic-resources/academic-integrity-and-grievances/academic-honor-policy)

Americans With Disabilities Act:

Florida State University (FSU) values diversity and inclusion; we are committed to a climate of mutual respect and full participation. Our goal is to create learning environments that are usable, equitable, inclusive, and welcoming. FSU is committed to providing reasonable accommodation for all persons with disabilities in a manner that is consistent with the academic standards of the course while empowering the student to meet the integral requirements of the course. Students with disabilities needing academic accommodation should: (1) register with and provide documentation to the Office of Accessibility Services; and (2) request a letter from the Office of Accessibility Services to be sent to the instructor indicating the need for accommodation and what type; and (3) meet (in person, via phone, email, skype, zoom, etc...) with each instructor to whom a letter of accommodation was sent to review approved accommodations. Please note that instructors are not allowed to provide classroom accommodations to a student until appropriate verification from the Office of Accessibility Services has been provided. This syllabus and other class materials are available in an alternative format upon request. For the latest version of this statement and more information about services available to FSU students with disabilities, contact the:

Office of Accessibility Services
874 Traditions Way
108 Student Services Building
Florida State University
Tallahassee, FL 32306-4167
(850) 644-9566 (voice)
(850) 644-8504 (TDD)
oas@fsu.edu
https://dsst.fsu.edu/oas

Academic Success:

Your academic success is a top priority for Florida State University. University resources to help you succeed include tutoring centers, computer labs, counseling and health services, and services for designated groups, such as veterans and students with disabilities. The following information is not exhaustive, so please check with your advisor or the Department of Student Support and Transitions to learn more.

CONFIDENTIAL CAMPUS RESOURCES:

centers and programs are available to assist students with navigating stressors that might impact academic success. These include the following:

Victim Advocate Program
University Center A, Rm. 4100
(850) 644-7161
Available 24/7/365
Office Hours: M-F 8-5
https://dsst.fsu.edu/vap

Counseling and Psychological Services (CAPS)

Florida State University’s Counseling and Psychological Services (CAPS) primary mission is to address psychological needs and personal concerns, which may interfere with students’ academic progress, social development, and emotional well-being. The following in-person and virtual (tele-mental health) services are available to all enrolled students residing in the state of Florida:

  1. Individual therapy

  2. Group therapy

  3. Crisis Intervention

  4. Psychoeducational and outreach programming

  5. After hours crisis-hotline

  6. Access to community providers for specialized treatment

Call 850-644-TALK (8255) for more information on how to initiate services.

Counseling and Psychological Services
250 Askew Student Life Center
942 Learning Way
(850) 644-TALK (8255)
Walk-in and Appointment Hours:
M-F 8 am – 4 pm
https://counseling.fsu.edu/

Services at UHS are available to all enrolled students residing in Florida:

The mission of University Health Services (UHS) is to promote and improve the overall health and well-being of FSU students. UHS provides a coordinated continuum of care through prevention, intervention, and treatment. Services include general medical care, priority care, gynecological services, physicals, allergy injection clinic, immunizations, diagnostic imaging, physical therapy, and a medical response unit. The Center for Health Advocacy and Wellness (CHAW) assists students in their academic success through individual, group, and population-based health and wellness initiatives. Topics include wellness, alcohol and other drugs, hazing prevention, nutrition and body image, sexual health, and power based personal violence prevention. For more information, go to uhs.fsu.edu.

University Health Services
Health and Wellness Center
960 Learning Way
Tallahassee, FL 32306
Hours: M-F, 8 am– 4 pm
(850) 644-6230
https://uhs.fsu.edu/

Free Tutoring from FSU

On-campus tutoring and writing assistance are available for many courses at Florida State University. For more information, visit the Academic Center for Excellence (ACE) Tutoring Services, for a comprehensive list of on-campus tutoring options, see https://ace.fsu.edu/tutoring or contact tutor@fsu.edu. High-quality tutoring is available by appointment and on a walk-in basis. These services are offered by tutors trained to encourage the highest level of individual academic success while upholding personal academic integrity.

Syllabus Change Policy

Except for changes that substantially affect the implementation of the evaluation (grading) statement, this syllabus is a guide for the course and is subject to change with advance notice.

Statement on Public Health Protocols

Class meets in person. If necessary, however, we will shift to remote instruction. There are currently no mask mandates in place at FSU, but if you feel more secure wearing a mask do so. If you feel sick please let me know by email and stay home. You can find up-to-date guidance at: https://stayhealthy.fsu.edu.

Lectures: Topic overview

Course material will be on CANVAS and also on my own website https://peterbeerli.com (classes)

  1. Processes and patterns

    • Population genetics: Wright-Fisher population models, Moran model, coalescence theory, genetic drift, gene flow, selection;

    • Phylogenetics: tree structures, speciation, birth/death models, Gene tree versus Species tree

    • Mutation models: real data (microsatellite markers, SNPs, sequences), modeling data, mutation/substitution model

    • Simulation of data

  2. Inference:

    • Parsimony and Distance methods

    • Maximum likelihood, Bayesian inference, Markov chain Monte Carlo,

    • Approximate Bayesian Computation

    • Model selection

    • Bootstrap/Jacknife

Each topic will include computational algorithms, problematic aspects such as convergence, biases, main focus will be on Bayesian and maximum likelihood methods.

Homework/Assignments

Homework assignment (each will be 10 points) follow the weekly outline and usually will be given on Thursdays, and expected to be turned in on next Thursday morning. The project consists of an outline (10 points), a presentation (15 points) and a report (not more than 8 pages) (15 points).

Lecture Schedule

<thead> </thead> <tbody> </tbody>
Week days Topic Practice
1 8/27,29 intro/tree chatgpt,writing and reading trees
2 9/3,5 optimality/tree search counting trees
3 9/10,12 parsimony (fitch, sankoff) impl. Fitch with chatgpt
4 9/17,19 mutation models distance methods
5 9/24,26 mutation models (finite vs infinite sites models)
6 10/1,3 likelihood creating a likelihood program
7 10/8,10 rate heterogeneity
8 10/15,17 bootstrap/jacknive
9 10/22,24 Bayesian inference
10 10/29,31 Priors Approximate Bayes sampler
11 11/5,7 MCMC
12 11/12,14 Coalescence 1 simulation of trees and sequences
13 11/19,21 Coalescence 2 estimation of population size
14 11/26 Project time
15 12/3,5 Project time (presentation)

Peter Beerli, August 2024

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