Thomas Giarla

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Genomics at Siena College

Course Overview

We are offering Bio400: Genomics and Bioinformatics for the first time at Siena College in Spring 2017. This course will be focused on GEP-related projects. Students will work on their own finishing and annotation projects as part of the course.


Lessons Learned and Future Plans

Syllabus for Bio400: Genomics and Bioinformatics

Biology 400: Genomics and Bioinformatics


Professor: Dr. Tom Giarla

Classroom and Meeting Time: Roger Bacon 122, Thursdays, 4:10–7:10pm


Welcome to Biology 400: Genomics and Bioinformatics! This course will be an exploration of the theories explaining the function and evolution of genomes (Genomics) alongside hands-on application of the computational tools biologists use to understand them (Bioinformatics). As part of this class, students will take on their own part of a larger genomics research project investigating the evolution of Drosophila chromosomes. This highly collaborative lecture/computer lab hybrid course will encourage students to work together to solve real research problems, eventually forming the backbone for a scientific publication with student co-authors.


Learning Goals: By the end of the semester, students will (1) refine a genome assembly and understand the bioinformatic tools used to construct genomes, (2) annotate part of a Drosophila genome and understand the types of evidence biologists use to identify functional elements within the genome, (3) become familiar with UNIX-based manipulation and processing of data files, and (4) understand the core research question that their work is contributing to.


Course Website


Up-to-date information about the course (including grades, hand-outs, and files) will be available online via Blackboard. All written assignments must be uploaded to Blackboard for submission—not as an email attachment. I will upload comments on your work directly to the Blackboard site.


Attendance & Expectations


Our class only meets 13 times over the course of the whole semester. As such, attending class is absolutely essential to attaining a high grade in the course, and I will take attendance. Please let me know in advance if you are not able to attend class due to illness, emergency, or some other legitimate reason. Given our time constraints, please do not expect class to ever let out early. To receive participation points, you must be present and working for the whole three-hour period.


Optional Textbook


Optional: Pevsner, Jonathan. (2015). Bioinformatics and Functional Genomics, 3rd Edition. Wiley-Blackwell.



I will assign grades based on the cut-offs below. If you find a tabulation error in my grading, please make note of the error on a short, separate piece of paper and attach it to the original assignment. If you believe that I graded something unfairly, submit your argument in writing, and I will consider re-grading the entire assignment. All late assignments will lose 25% of the points immediately, and 10% more for each additional day late.


A         93 – 100%                   B-        80 – 82.9%                  D+       67 – 69.9%

A-        90 – 92.9%                  C+       77 – 79.9%                  D         63 – 66.9%

B+       87 – 89.9%                  C         73 – 76.9%                  D-        60 – 62.9%

B         83 – 86.9%                  C-        70 – 72.9%                  F          0  –  59.9%




Portion of Final Grade




Homework (8 Assignments)



Finishing Report



Chimp Chunk Report and Presentation



Annotation Report







Course Schedule



Lecture Topic

In-Class Activities

Homework Due

Project Due

Jan. 19

Topic 1: Introduction to Genomics & Bioinformatics

  • UNIX Tutorial
  • Workshop 1: Practice with Consed
  • GEP Pre-Class Survey (optional)



Jan. 26

Topic 2: DNA Sequencing & Genome Assembly

  • Overview of finishing protocol
  • Start Homework 2

Homework 1: Introduction to UNIX (10pts)


Feb. 2

Topic 3: Prokaryotic Transcription & Translation (Dr. Sterne-Marr)

  • Discussion of Finishing Project goals and expectations
  • Distribution of individual Finishing Projects
  • Work on Genome Finishing Project

Homework 2: Drosophila Sequence Improvement Problem Set (20pts)


Feb. 9

Topic 4: Eukaryotic Genomes

(Dr. Sterne-Marr)

  • Work on Finishing Project

Homework 3: Detecting and Interpreting Genetic Homology (15pts)


Feb. 16


  • Workshop 2: Chimp BAC Analysis
  • Work on Finishing Project



Feb. 23

Winter Break – No Class



Finishing Report Due (100pts)

Mar. 2

Topic 5: Chromatin Structure

  • Discussion of Chimp Chunk Project goals and expectations
  • Distribution of group Chimp Chunk Projects
  • Work on Chimp Chunk Project



Mar. 9

Topic 6: Gene Finding

  • Workshop 3: A Simple Annotation Exercise
  • Work on Chimp Chunk Project

Homework 4: What is a Gene? (15pts)


Mar. 16

Topic 7: Transcriptomics

  • Student Chimp Chunk Presentations
  • Workshop 4: Annotation of a Drosophila Gene


Chimp Chunk Report and In-Class Presentation Due (75pts)

Mar. 23

Topic 8: Genome Annotation

  • Example Annotation Presentations by Research Assistants
  • Discussion of Annotation Project goals and expectations
  • Distribution of individual Annotation Projects

Homework 5: Transcription, Part I (20pts)


Mar. 30

Topic 9: Searching for Transcription Start Sites

  • Workshop 5: Annotation of Transcription Start Sites

Homework 6: Transcription, Part II (15pts)


Apr. 6


  • Annotation Project progress check
  • Work on Annotation Project

Homework 7: Splicing (15pts)


Apr. 13

Easter Break – No Class




Apr. 20

Topic 10: GEP Findings: The Bigger Picture

  • Annotation Project progress check
  • Work on Annotation Project

Homework 8: Translation (15pts)


Apr. 27


  • GEP Post-Class Survey (optional)
  • Work on Annotation Project



May 1

Monday – No Class



Annotation Report Due (150pts)