Difference between revisions of "Syllabus"

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ISC5317/ISC4933:
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<h1 class="unnumbered"
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id="graduateundergraduate-course-computational-evolutionary-biology">
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= Computational Evolutionary Biology =
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<strong>Graduate/Undergraduate course:<br />
−
 
+
Computational Evolutionary Biology</strong></h1>
−
Section marked with '''*''' differentiate between the graduate section requirements and the undergraduate section requirements
+
<h2 class="unnumbered" id="class-meeting">Class Meeting</h2>
−
 
+
<p>Lectures:<br />
−
== Class Meeting ==
+
Tuesdays and Thursdays 1:20-2:35 PM Dirac Science Library Room 422</p>
−
 
+
<h2 class="unnumbered" id="instructor">Instructor</h2>
−
Lectures: Tuesdays and Thursdays 11:00AM-12:15 PM Dirac Science Library Room 152
+
<p>Peter Beerli<br />
−
 
+
Office: 150-T DSL<br />
−
== Instructor ==
+
Email: beerli@fsu.edu<br />
−
 
+
Cell: (850) 559-9664 [Text appreciated]</p>
−
Peter Beerli<br> Office: 150-T DSL<br> Email: beerli@fsu.edu<br> Phone: (850) 559-9664
+
<h2 class="unnumbered" id="office-hours">Office Hours</h2>
−
 
+
<p>Monday usually 1:00-3:00 PM by appointment.</p>
−
== Class Assistant ==
+
<h2 class="unnumbered" id="objectives">Objectives</h2>
−
 
+
<p>This course will introduce students to methods used in phylogenetics
−
Kyle Shaw<br> Office: 150-J DSL<br> Email: shawk3@outlook.com<br> Phone: TBA
+
and population genetics and writing computer programs using these
−
 
+
methods. The primary objectives of the course are:</p>
−
== Office Hours ==
+
<ol>
−
 
+
<li><p>to expose students to a large set of modern methods used in
−
* Peter Beerli: by appointment (email: beerli@fsu.edu or text to 850 559 9664); or just come to my office, If do not have a meeting I will have time for you.
+
theoretical evolutionary biology and learn about the details of often
−
* Kyle Shaw: we will set up an open lab session every week so that students can get help on python and the assignments.
+
used methods in phylogenetic and population genetics analyses.</p></li>
−
 
+
<li><p>to introduce students to the programming aspects of the field.
−
== Objectives ==
+
Students will learn and use the programming language Python to develop
−
 
+
scripts and to understand the details of the methods. Learning Python
−
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:
+
will be assisted using AI technology (chatGPT) which we will use
−
 
+
extensively to write code.</p></li>
−
# 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.
+
<li><p>to empower students to develop programming and analysis skills
−
# 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.
+
that involve the development of scripts to change data format, execute
−
# to empower students to develop programming and analysis skills that involve development of scripts to change data format, execute applications, and analyze results.
+
applications, and analyze results.</p></li>
−
 
+
</ol>
−
== Content ==
+
<h2 class="unnumbered" id="rational-for-the-objectives">Rational for the
−
 
+
objectives</h2>
−
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>Current biological studies have started to emphasize the importance
−
 
+
of data analytics, but still, most courses simply use packaged programs,
−
== Textbook ==
+
leaving the students at a disadvantage if no courses exist that improve
−
 
+
the computational skills of students. This course prepares students for
−
We will have no textbook, but we have extensive handouts available through the course website.
+
such a challenge.</p>
−
 
+
<h2 class="unnumbered" id="content">Content</h2>
−
== Grading ==
+
<p>Advanced computational methods are becoming increasingly important in
−
 
+
biology. A wide range of applications — including, for instance,
−
* Grades will be based on students’ execution of the 5 (programming) assignments, each of which involves understanding the algorithms, code design, and program documentation <br>[100 points each<br>]
+
identifying pathogens, tracing viral transmission pathways, and
−
* Either two students or a single student will work on a project on their own during the last 4 weeks of the semester and give a short presentation of their work during the last second two classes periods. I expect that group projects are twice as large as single student projects <br>[100 points for the report and 100 points for the presentation<br>]
+
reconstructing the geographic expansion of humans out of Africa — rely
−
* We will have a theory test on November 7th (midterm). <br>[100 points<br>]
+
on evolutionary inference. This course will cover the methods currently
−
* There will be no final exam, the project substitutes for a final examination. The total number of points is 800.
+
used for evolutionary inference, the stochastic models and inference
−
 
+
principles they are based on, and how they are implemented in practice.
−
'''*''' 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”. The grade of ndergraduate student is calculated as 110% of the graduate grade, for example if the grade is a total of 745 points, a graduate student will receive 655/800= 0.81875 <math>\rightarrow</math> B; an undergraduate student will receive 655/800*1.1= 0.900625 <math>\rightarrow</math> A.
+
The students will get hands-on experience in developing computational
−
 
+
software. We expect that the students leave the course with the
−
== Missed/Late Assignments ==
+
necessary skills to develop their own ideas and develop projects based
−
 
+
on simulated data sets and scripts.</p>
−
Deadlines for assignments will be announced in class; late assignments will be accepted for full grade only in cases of illness or death in the family. 5% of the total points (100pt) are deducted per day for late assignments.
+
<h2 class="unnumbered" id="textbook">Textbook</h2>
−
 
+
<p>We do not use a textbook, but if you feel that you need a book use
−
== University Attendance Policy ==
+
this one: Yang, Z. 2006. Computational Molecular Evolution. Oxford
−
 
+
University Press, Oxford, England. (Book website:
−
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.
+
http://abacus.gene.ucl.ac.uk/CME/)</p>
−
 
+
<h2 class="unnumbered" id="grading">Grading</h2>
−
== Academic Honor Policy ==
+
<ul>
−
 
+
<li><p>Grades will be based on students’ execution of programming
−
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 ... <br>[to<br>] strive for personal and institutional integrity at Florida State University.&quot; (Florida State University Academic Honor Policy, found at http://dof.fsu.edu/honorpolicy.htm.)
+
assignments, each of which involves understanding the algorithms, code
−
 
+
design, and program documentation [10 points each]</p></li>
−
== Americans With Disabilities Act ==
+
<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
−
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:
+
in the last regular lab-meeting. [15 points for the report and 15 points
−
 
+
for the presentation]</p></li>
−
== Tutoring in class ==
+
<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
−
The TA will have a weekly session of two hours to help with assignments and Python tutoring, use this resource.
+
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
−
== Free Tutoring from FSU ==
+
affect the grade for the assignment either positively or
−
 
+
negatively.</p></li>
−
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.
+
<li><p>There will be no mid-term and final exams; the project
−
 
+
substitutes for a final examination.</p></li>
−
== Syllabus Change Policy ==
+
</ul>
−
 
+
<p>A student who accumulates 90% or more of the possible points will
−
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.
+
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
−
== Lectures: Topic overview ==
+
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
−
# Processes and patterns
+
possible points will receive a grade of "D", and a student who
−
#* Population genetics: Wright-Fisher population models, coalescence theory;
+
accumulates less than 60% of the possible points will receive a grade of
−
#* Phylogenetics: tree structures, speciation, Gene tree versus Species tree
+
"F".</p>
−
#* Mutation models: mutation/substitution model
+
<h2 class="unnumbered" id="missedlate-assignments">Missed/Late
−
#* Simulation of data
+
Assignments</h2>
−
# Inference:
+
<p>Deadlines for assignments will be announced in class; late
−
#* Parsimony and Distance methods
+
assignments will be accepted for full grade only in meidcal cases. 10%
−
#* Maximum likelihood, Bayesian inference, Monte Carlo, Markov chain Monte Carlo,
+
of the points are deducted per day for late assignments; An assignment 1
−
#* Model selection
+
day late will be 90% of the points, 2 days late 80%, ... If you think
−
#* Bootstrap/Jacknife
+
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
−
Each topic will include computational algorithms, problematic aspects such as convergence, biases, main focus will be on Bayesian and maximum likelihood methods.
+
evening of the due date.</p>
−
 
+
<h2 class="unnumbered" id="university-attendance-policy">University
−
== Assignments ==
+
Attendance Policy:</h2>
−
 
+
<p>Excused absences include documented illness, deaths in the family,
−
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 to the ones shown below:
+
and other documented crises, call to active military duty or jury duty,
−
 
+
religious holy days, and official University activities. These absences
−
# Read and write a tree structure
+
will be accommodated in a way that does not arbitrarily penalize
−
# Simulate data on a tree
+
students who have a valid written excuse. Consideration will also be
−
# Simulate data using the coalescent
+
given to students whose dependent children experience serious
−
# Construct an ABC sampler to estimate the effective population size
+
illness.</p>
−
# Model selection using the program MIGRATE
+
<h2 class="unnumbered" id="academic-honor-policy">Academic Honor
−
# 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.
+
Policy:</h2>
−
 
+
<p>The Florida State University Academic Honor Policy outlines the
−
* Undergraduate students can leave out one of the assignments (1-5).
+
University’s expectations for the integrity of student’s academic work,
−
 
+
the procedures for resolving alleged violations of those expectations,
−
== Lecture Schedule ==
+
and the rights and responsibilities of students and faculty members
−
 
+
throughout the process. Students are responsible for reading the
−
# Introduction. Trees and tree representation (Aug. 29)
+
Academic Honor Policy and for living up to their pledge to “. . . be
−
# Python and trees (Aug. 31)
+
honest and truthful and . . . [to] strive for personal and institutional
−
# Parsimony (Sep 5)
+
integrity at Florida State University.” (Florida State University
−
# Python and parsimony (Sep 7)
+
Academic Honor Policy, found at
−
# Searching for the best tree(s) (Sep 12)
+
http://fda.fsu.edu/academic-resources/academic-integrity-and-grievances/academic-honor-policy)</p>
−
# Substitution models and distance (Sep 14)
+
<h2 class="unnumbered" id="americans-with-disabilities-act">Americans
−
# Substitution models general Sep 19)
+
With Disabilities Act:</h2>
−
# Substitution model exercise Sep 21)
+
<p>Florida State University (FSU) values diversity and inclusion; we are
−
# Rate variation and more substitution models Sep 26)
+
committed to a climate of mutual respect and full participation. Our
−
# Maximum Likelihood (Sep 28)
+
goal is to create learning environments that are usable, equitable,
−
# Maximum Likelihood (Oct 3)
+
inclusive, and welcoming. FSU is committed to providing reasonable
−
# Bayesian inference (Oct 5)
+
accommodation for all persons with disabilities in a manner that is
−
# Markov chain Monte Carlo (Oct 10)
+
consistent with the academic standards of the course while empowering
−
# ABC – approximate Bayesian computing (Oct 12)
+
the student to meet the integral requirements of the course. Students
−
# The coalescent (Oct 17)
+
with disabilities needing academic accommodation should: (1) register
−
# Coalescent simulation and extensions to the coalescent (Oct 19)
+
with and provide documentation to the Office of Accessibility Services;
−
# Gene tree vs Species tree (Oct 24)
+
and (2) request a letter from the Office of Accessibility Services to be
−
# Gene tree vs Species tree (Oct 26)
+
sent to the instructor indicating the need for accommodation and what
−
# Model Selection (Oct 31)
+
type; and (3) meet (in person, via phone, email, skype, zoom, etc...)
−
# Bootstrap/Jacknife (Nov 2)
+
with each instructor to whom a letter of accommodation was sent to
−
# Review session (Nov 7)
+
review approved accommodations. Please note that instructors are not
−
# Mid term (Nov 9)
+
allowed to provide classroom accommodations to a student until
−
# Project (Nov 14)
+
appropriate verification from the Office of Accessibility Services has
−
# Project (Nov 16)
+
been provided. This syllabus and other class materials are available in
−
# Project (Nov 21)
+
an alternative format upon request. For the latest version of this
−
# Project (Nov 28)
+
statement and more information about services available to FSU students
−
# Project (Nov 30)
+
with disabilities, contact the:</p>
−
# Presentation (Dec 5)
+
<p>Office of Accessibility Services<br />
−
# Presentation (Dec 7)
+
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>
 +
<li><p>Individual therapy</p></li>
 +
<li><p>Group therapy</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>
 +
<p>Call 850-644-TALK (8255) for more information on how to initiate
 +
services.</p>
 +
<p>Counseling and Psychological Services<br />
 +
250 Askew Student Life Center<br />
 +
942 Learning Way<br />
 +
(850) 644-TALK (8255)<br />
 +
Walk-in and Appointment Hours:<br />
 +
M-F 8 am – 4 pm<br />
 +
https://counseling.fsu.edu/<br />
 +
</p>
 +
<h2 class="unnumbered"
 +
id="services-at-uhs-are-available-to-all-enrolled-students-residing-in-florida">Services
 +
at UHS are available to all enrolled students residing in Florida:</h2>
 +
<p>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.</p>
 +
<p>University Health Services<br />
 +
Health and Wellness Center<br />
 +
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>
 +
<li><p>Processes and patterns</p>
 +
<ul>
 +
<li><p>Population genetics: Wright-Fisher population models, Moran
 +
model, coalescence theory, genetic drift, gene flow, selection;</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>
 +
</ul></li>
 +
<li><p>Inference:</p>
 +
<ul>
 +
<li><p>Parsimony and Distance methods</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>Bootstrap/Jacknife</p></li>
 +
</ul></li>
 +
</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>
 +
<h2 class="unnumbered"
 +
id="homeworkassignments">Homework/Assignments</h2>
 +
<p>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).</p>
 +
<h2 class="unnumbered" id="lecture-schedule">Lecture Schedule</h2>
 +
<table>
 +
<thead>
 +
<tr>
 +
<th style="text-align: center;">Week</th>
 +
<th style="text-align: left;">days</th>
 +
<th style="text-align: left;">Topic</th>
 +
<th style="text-align: left;">Practice</th>
 +
</tr>
 +
</thead>
 +
<tbody>
 +
<tr>
 +
<td style="text-align: center;">1</td>
 +
<td style="text-align: left;">8/27,29</td>
 +
<td style="text-align: left;">intro/tree</td>
 +
<td style="text-align: left;">chatgpt,writing and reading trees</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">2</td>
 +
<td style="text-align: left;">9/3,5</td>
 +
<td style="text-align: left;">optimality/tree search</td>
 +
<td style="text-align: left;">counting trees</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">3</td>
 +
<td style="text-align: left;">9/10,12</td>
 +
<td style="text-align: left;">parsimony (fitch, sankoff)</td>
 +
<td style="text-align: left;">impl. Fitch with chatgpt</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">4</td>
 +
<td style="text-align: left;">9/17,19</td>
 +
<td style="text-align: left;">mutation models</td>
 +
<td style="text-align: left;">distance methods</td>
 +
</tr>
 +
<tr>
 +
<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
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108 Student Services Building
Florida State University
Tallahassee, FL 32306-4167
(850) 644-9566 (voice)
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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
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(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
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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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