BIO Assignment 1 2011
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Contents
Assignment 1 - Databases and Molecular Models
Introduction
In this assignment we will introduce some key databases for bioinformatics that we will refer to throughout the course. You will receive more information on these databases as the course progresses, but you should be familiar in principle with their contents and services from the outset. Also, to enhance your course experience, you should familiarize yourself with a molecular graphics viewer and practice viewing molecules in stereo.
Submission and due date
Prepare a Microsoft Word document with a title page that contains:
- your full name
- your Student ID
- your e-mail address
Copy the assessment part of the assignment into the document. save it with a filename of:
A1_{lastname}.{firstname}.doc
(for example my first assignment would be named: A1_steipe.boris.doc)
and e-mail the document to boris.steipe@utoronto.ca before the due date.
With the number of students in the course, we have to economize on processing the assignments. Thus we will not accept assignments that are not prepared as described above. If you have technical difficulties, contact me.
The due date for the assignment is Monday, October 1. at 11:00 in the morning.
Grading
Marks for this assignment are self assessed. We expect your honesty, but you can expect that the skills you obtain through this assignment will also be required for the final exam.
Don't wait until the last day to find out there are problems! Assignments that are received past the due date will have one mark deducted and an additional mark for every full twelve hour period past the due date. Assignments received more than 5 days past the due date will not be assessed. If you need an extension, you must arrange this beforehand.
The marks you receive will
- count directly towards your final marks at the end of term, for BCH441 (undergraduates), or
- be divided by two for BCH1441 (graduates).
Key databases
NAR DB and Web Service issues (1 mark)
Access the NAR issues and read.
Entrez and the NCBI (2 marks)
Visit the NCBI website at http://www.ncbi.nlm.nih.gov/
Look for the site-map and explore the contents of this site, the databases, the services and its other offerings. Browse across the different sections and set yourself a specific objective so you are confident you know what this part is and does. Expect to spend more than two hours on this task.
For example, you might have:
- looked at least at two Coffee Break tutorials and know what the others contain
- familiarized yourself with the search field tags in PubMed to the degree that you know how to formulate a specific search, for example to retrieve review articles that mention the cell cycle in their title, which are about saccharomyces cerevisiae , that are not more than two years old
- tried searching for crossreferences to the YER111C gene using the Entrez system
- used the map viewer to explore the region between 370 and 400 KB on yeast chromosome V
- etc.
Use Entrez ...
The EBI (1 mark)
Visit the EBI website at http://www.ebi.ac.uk/
Look for the site-map and explore the contents of this site, the databases, the services and its other offerings. Browse across the different sections and set yourself specific objectives so you are confident you know what each section is and does. Expect to spend more than two hours on this task.
For example, you might have:
- browsed through the tutorials (e.g. the lectin tutorial) in the education section of the Macromolecular Structure Database (MSD)group
- used the e! Ensembl browser to compare your experience in exploring yeast chromosomeV:370000-400000
- explored crossreferences to the yeast Swi4 protein using the SRS system
- browsed through the Interpro Molecule of the Month articles and read the article on TATA-box binding protein
- looked at the 2can tutorial pages and explored the tutorial on database browsing
- etc.
The PDB (1 mark)
Visit the PDB website at http://www.pdb.org/
Browse across the different sections and set yourself a specific objective so you are confident you know what this part is and does. Look for the "About PDB" page and explore the page. Explore the links on the "Education" page to see where you might fill in gaps in your knowledege of structural molecular biology. From the homepage, find a protein of your choice (eg. the yeast Swi6 or Mbp1 protein) and explore the information that is available for it. Expect to spend more than an hour on this task.
For example, you might have:
- worked through the PDB query tutorial
- browsed through the Molecule of the Month articles and studied the entry on TATA-box binding proteins
- and explored structures entries for 1SW6, 1E0B and 1BM8
- etc.
KEGG (1 mark)
Data integration across a variety of databases is a major challenge for the data-management side of bioinformatics. You have come across two solutions above: the NCBI Entrez system and the EBI SRS system. Here is another solution to this problem: the EBI BioMart system.
- Access the BioMart server at http://www.biomart.org
- Follow at least two links into BioMart databases (e.g. ensembl and HapMap)
- Explore
Molecular graphics
Access the Rasmol tutorial at http://biochemistry.utoronto.ca/steipe/bioinformatics/tutorials/rasmol_tutorial.html Install Rasmol(Linux), RasMac (Macintosh), or RasTop(Windows) on your computer.
Work through the tutorial.
VMD (1 marks)
Access the Rasmol tutorial at http://biochemistry.utoronto.ca/steipe/bioinformatics/tutorials/rasmol_tutorial.html Install Rasmol(Linux), RasMac (Macintosh), or RasTop(Windows) on your computer.
Work through the tutorial.
Stereo vision (3 marks):
Use the hints given in the stereo vision section of the Rasmol tutorial and practice viewing molecules in stereo. Make sure that you use the Rasmol command
set stereo -5
to display molecules for divergent ("wall-eyed", not "cross-eyed") stereo view. Practice at least ...
- two times daily,
- for 3-5 minutes each session,
- for at least twelve days (twentyfour sessions) between now and the due date of the assignment.
Keep up your practice after the assignment. Stereo viewing will be required in the final exam.
You will receive 1 mark for every 8 sessions (4 days) of practice you have completed (max. 3 marks). Use different molecules and try them with different colouring and renderings. You will find a list suggesting interesting molecules on the tutorial page.
Record your progress on a sheet of paper. Make sure you also record the information for the supplementary questions you need to turn in (see below).
Note: do not go through this assignment mechanically. If you are not making any progress, contact me so we can help you on the right track.
Assessment
NCBI: I have explored the NCBI Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the NCBI site in detail (0 marks).
EBI: I have explored the EBI Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the EBI site in detail (0 marks).
PDB: I have explored the PDB Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the PDB site in detail (0 marks).
KEGG: I have accessed the KEGG site and familiarized myself with the functionality of at least two BioMart databases. I understand some of the issues of data integration and how they are addressed through BioMart. (1 mark).
or
I did not find the time to explore the KEGG site (0 marks).
Copy and paste from the following statements the one that best characterizes your situation:
VMD: I have successfully completed the first part of the VMD tutorial; I understand the purpose and use of all the forms used in the tutorial examples and can confidently use the program for my own visualization tasks (2 marks).
or
I have worked with the VMD tutorial. Nevertheless, I am not confident with the forms and their use and before I can use it for my own purposes I will need additional training (1 mark).
or
I have not done this part of the assignment (0 marks).
Copy the following statement into your assignment and fill in the blanks truthfully.
Stereo Vision: I have practiced stereo viewing twice daily on _____ days for a total of _____ practice sessions (maximum 3 marks for 24 sessions).
Supplementary questions (these will not be marked):
I have been able to visualize a 3D image in focus for the first time on day ___. I have been able to view molecules in stereo comfortably since day ___. Currently I am able to view molecules in stereo on screen and on paper with ease / with some effort / with difficulty / rarely / not at all.
[End of assignment]
