Assignment submission details

Assignment preparation and submission

Preparation

Your assignment is to be prepared as an electronic document, except where explicitly stated otherwise. Prepare a Microsoft Word document with a title page that contains:

• your full name
• your Student ID
• your e-mail address
• the organism name you have been assigned (in Assignment 2 and later)

• Save your document with a filename of: A{X}_{family name}.{given name}.doc

(for example my second assignment would be named: "A2_steipe.boris.doc". Please don't switch the order of your given name and family name.

• Make sure to submit your assignments as .doc files only, i.e. use the MSWord binary format prior to the 2007 format change. Do not submit the Office Open XML package format files, with the .docx or .docx.zip extension, these files will not be accepted. .rtf files will also be rejected.

General documentation

As one part of your assignment, you should submit documentation of your activities. Do this like you would write a lab notebook. This is not intended to be a formal lab report, but a point-form record of your activities. Write this as notes to yourself.

For each task:

• Write a header.

Please use the same header number and text of the assignment and keep the sequence of tasks given in the assignment. Keep distinct tasks in separate paragraphs.

• State the objective.

In one brief sentence, restate what this task is to achieve.

• Document the procedure.

Note what you have done, as concisely as possible. Give enough information so that anyone could reproduce unambiguously what you have done.

• Document your results.

You can distinguish different types of results:

• • Static data does not change over time and it may be sufficient to note a reference to the result. For example, there is no need to copy a genbank record into your documentation, it is sufficient to note the accession number or the GI number.
  • Variable data can change over time. For example the results of a BLAST search depend on the sequences in the database. A list of similar structures may change as new structures get solved. In principle you want to record such data, to be able to reproduce at a later time what your conclusions were based on. But be selective in what you record. For example you should not paste the entire set of results of a BLAST search into your asignment, but only those matches that were important for your conclusions. Indiscriminate pasting of irrelevant information may cause deduction of marks.
  • Analytic results

The results of sequence analyses, alignments etc. in general get recorded in your documentation. Again: be selective. Record what is important.

• Note your conclusions.

An analysis is not complete unless you conclude something from it. Are two sequences likely homologues, or not? Does your protein contain a signal-sequence or does it not? Is a binding site conserved, or not? The analysis gives you data, in your conclusion you provide the interpretation of what the data means in the context of your objective. Sometimes we will ask you to elaborate on an analysis and conclusion. But this does not mean that when we do not, you don't need to interpret your data.

Specific questions

At some points in the assignment you will be asked for more detailed analysis. Presnt you analysis as follows:

• Present your data and its interpretation.
• Discuss alternative interpretations.
• Provide a conclusion.

Be concise.

 

Submission

• Keep your submissions concise and simple.
• Avoid unnecessary formatting.

Preparation of images

Use JPG, GIF, PNG or SVG images.

Never paste screendumps. Save images, and embed them in a compressed file format.

Image sizes are measured in pixels - 600px across is sufficient for the assignment, resolutions are measured in dpi (dots per imperial inch) - 72 dpi is the standard resolution for images that are viewed on a monitor; the displayed size may be scaled (in %) by an application program: stereo images are best presented so that equivalent points are approximately 6 cm apart; images can be stored uncompressed as .tiff or .bmp, or compressed as .gif or .jpg or .png. .gif is useful for images with large, monochrome areas and sharp, high-contrast edges due to the LZW compression algorithm it uses; .jpg or .jpeg is preferred for images with shades and halftones such as the structure views required in the course assignments, it has excellent application support and is the most versatile general purpose image file format currently in use; .tiff or .tif is preferred to archive master copies of images in a lossless fashion, use LZW compression for TIFF files if your system/application supports it; The .png format is an open source alternative for lossless, compressed images, application support is growing but still variable. .bmp is not preferred for really anything, it is bloated in its (default) uncompressed form and primarily used only because it is simple to code. If you have technical difficulties, post your questions to the list and/or contact me.

Keep the overall size of your submission below 1.5 MB.

We will deduct marks for larger submissions, or we may reject the submission outright.

Preparation of stereo views

When molecular images are required, always submit stereo views, even if this was not explicitly required in the text of the assignment. All required stereo views are to be presented as divergent (parallel, side-by-side) stereo frames (left eye's view in the left frame), even if you use cross-eyed views for yourself (three-panel views are acceptable).

Keep your images uncluttered and expressive

Turn off the axes if they are not needed and scale the molecular model to fill the available space of your image well. Orient views so they illustrate a point you are trying to make. Emphasize residues that you are writing about with a contrasting coloring scheme. Add labels, where residue identities are not otherwise obvious. Turn off side-chains for residues that are not important.

General document requirements

Macros

Your document must not contain macros. Please turn off and/or remove all macros from your Word document; we will disable macros, since they pose a security risk but since files are read-only once macros are disabled, we may also deduct marks for the additional overhead that this requires.

Group work

Group-work on the assignment is explicitly encouraged but must be conducted in accordance with the University's code of academic standards. You must take full responsibility for the entirety of the submitted assignment, you must be familiar with the concepts and procedures your assignment pertains to as if you had executed them yourself, and you must not use copies of results of any materials you have received from others without properly referencing this fact. Omission of references is considered plagiarism and may result in academic misconduct procedures against both the submitter as well as the source. Please review the University's Code of Behaviour on Academic Matters, section B.i.1. for other applicable academic offences.

 

To submit, e-mail the document to boris.steipe@utoronto.ca before the due date.

Once your assignment has been received, you will receive an e-mail confirming that your assignment has been received. If I have not received your assignment by the due date, I will contact you. There is no need for you to request confirmation.

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.

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.

 

 

Grading

A total of 4 marks will be awarded, if your assignment addresses all requirements. A bonus mark can be awarded for particularly interesting findings, or insightful comments. A total of 2 marks can be subtracted for lack of form or for glaring errors. The marks you receive will

• count directly towards your final marks at the end of term, for BCH441 (undergraduates), or
• will be multiplied by 3/4 for BCH1441 (graduates).