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
• the organism name you have been assigned (in Assignment 2 and later)
• your e-mail address in case we need to communicate with you

• 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. Also, take note of the naming conventions: use underscores instead of blanks.

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

• 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.

Documentation: Lab-Notebook Style

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 actual activities. Write such documentation as notes to yourself.

For each task:

• Write a header.

Please use the same header number and text of the assignment and do not change 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.
  • Analysis 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 the results. 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 the 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 ask, you don't need to interpret your data.

Specific questions

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

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

Be concise.

 

Preparation of images

Don't paste uncompressed screendumps into your assignment. Save images separately in a compressed file format. Then use the Insert → Picture → From File ... function of MSWord to insert the image into your file.

Image types.

In principle, 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.

Image dimensions and resolution

Stereo images should have equivalent points approximately 6cm apart. It depends on your monitor how many pixels this corresponds to. The dimensions of an image are stated in pixels (width x height). My notebook screen has a native display resolution of 1440 x 900 pixels/23.5 x 21 cm. Therefore a 6cm separation on my notebook corresponds to ~260 pixels. However on my desktop monitor, 260 pixels is 6.7 cm across. For the assignments: adjust your stereo images so they are approximately at the the right separation and approximately 500 to 600 pixels across. Also, scale your molecules so they fill the available window.

Considerations for print (manuscripts etc.) are slightly different: for print output you can specify the output resolution in dpi (dots per inch). A typical print resolution is about 300 dpi: 6 cm separation at 300dpi is about 700 pixels. Print images should therefore be about three times as large in width and height as screen images.

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.

If you have technical difficulties, post your questions to the list and/or contact me.

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.

 

 

Submission

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

To submit, place your document into the shared Dropbox folder for the assignment before the due date. After the due date, the documents will be moved out of the shared folder for marking. All subsequent edits or uploads will be ignored, except if previously coordinated with me (e.g. extensions).

Due date and late marks

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 day 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 before the due date.

 

 

Grading

A total of 3 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 2/3 for BCH1441 (graduates).