840:153g/2008

Course Overview

This page is the PRELIMINARY homepage of the course titled "840:153g". Current version: Fall 2008! The page and course contents are still under development - please check back often!

We have 16 students in class which will work in teams of two throughout the semester. Each team will clone a hop (this is the name of the plant :-) gene, amplify it in E. coli and verify the integrity of a functional gene.

As a student, you have to select a gene from the NCBI database and clone the coding region only (no introns are allowed). In your team, you need to develop a strategy for cloning the gene, including a procedure for verification that you actually cloned the full coding region of the right gene. The approach must be written up in form of a research proposal and approved by the instructor before lab work can commence.

Each team will need to develop a website at OWW where the group describes its project (in form of the proposal). The project description should make up the first page of the online notebook. I also require that teams write a DAILY online lab notebook for EACH and EVERY lab session once lab work has started. This online notebook must contain all procedures carried out during the lab session, including description and discussion of results. It should also contain a brief description of the steps planned for the next session. Of course, everything must be relevant for the proposed work.

Getting Started with OWW

To get started with your online notebook, you have to apply for an account at OWW (which is free). Please write down your username and password from your confirmation email. After you obtained your account details, please go to the Project Page and start developing your project. There is help available in the left-handed navigation pane on how to use the WIKI.

Grading

A large and very important part of the class grade will be based on the online notebook. The notebook will be graded based on completeness, accuracy, and content. It will substitute for a paper lab notebook, although I strongly recommend to keep notes during each and every session (write down observations, calculations, remarks, etc.) The notebook has to be written at the day of the lab! No late entries (even 1 day) will be considered (the system we use gives time stamps !). Since each entry in OWW contains a time stamp and the name of user who writes it, this is very easy for me to monitor. Notebook writing is considered to be part of the work and therefore this work should be done during the lab. There will be lag times while experiments run and you should use those times for writing your notebook. The computer room is right next door.

Finally, I expect each group to clone their gene. If a group does not achieve it, the problems must be explained thoroughly in the notebook and evidence must be provided from the notebook that sufficient efforts have been undertaken to clone the gene. After all this is real science (none of the genes have been cloned) and there is no guarantee that any group will succeed. Therefore, keeping a good notebook is essential. The notebook will account for 40% of the grade and both partners receive the same grade for the notebook, weighed by a peer assessment. Both partners should therefore regularly take responsibility to develop a good notebook.

As the instructor, I will assign another 40% of the grade based everybody's individual contribution during class sessions (including preparation for class, discussion of experiments and results, timeliness, and teamwork). The remaining 20% will be given for the project presentation. One member of each team will give a midterm presentation (before spring break), the other member will give a final presentation (the week before finals). Both presentation should give an overview of what has been done - and achieved - in the project. It will be essential to provide experimental data and discuss them with classmates.

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