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| Two overlapping screenshots can be combined into a single image later. You don't have to do this yourself. | |
During the course of the semester, you will complete various aspects of your annotation project. We will collect your work via electronic submission and post it on the class website. This page is a guideline to electronic submission.
The final report to be submitted to Washington University at the end of the semester has a very specific format; your work posted on the class website will be the basis for this submission.
You can submit work at any time via email to pszauter@unm.edu.
If you are submitting large files or multiple files via email, you may encounter objections from LoboMail. You may wish to use a free file sharing service such as YouSendIt. YouSendIt requires you to register with an email address and password, but most simple file sharing services are free.
During class, you can submit work electronically by asking to save your work on the shared classroom hard drive. You can submit or save anything that you like this way. It is best if you collect all of your files into a single folder that has your name as its title.
A. Screenshots. On the Mac, you can take a screenshot of the full screen at any time using the Command-Shift-3 combination. You can take a screenshot of part of the screen using the Command-Shift-4 combination. These screenshots will typically be .png or .jpg files. You should always rename the screenshot something brief but descriptive that you record in your lab notebook, noting exactly what you did to get the results. For example, if you did a BLAST search, you should record the source of the query sequence, the BLAST program used, and the database searched or specific sequence used for a bl2seq alignment.
Many data displays occupy more screen space than can be seen on the screen of a laptop. In this case, take multiple screenshots that overlap. These will be combined into a single large image later, as shown below.
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| Two overlapping screenshots can be combined into a single image later. You don't have to do this yourself. | |
When submitting screenshots, please do not reduce the size of the images.
B. Text documents associated with images. For most results, you will want to create documents that are a mixture of text and images, as in the results of the Gene Prediction Exercise. There are several ways to do this.
1. Hypertext Markup Language (HTML). The class website is a collection of HTML pages (anything with a .html extension), images (typically .jpg), and some PDFs (.pdf). All of the HTML pages are written as raw HTML using a text editor called BBEdit (highly recommended). If you know how to write HTML, you can submit material as HTML documents with associated image files in a folder called "images."
If you plan to submit HTML pages, you might find it useful to examine the source code for selected pages of the class website. Most browsers have a feature that allows you to examine the page source.
2. Plain text. If you don't know how to write HTML, you can submit a text document as a plain text file. Microsoft Word will allow you to save a document as a text file rather than as a Word document. In your text file, you can indicate the location of specific images using a convention like this:
[insert BLASTN1.jpg here]
You can send the plain text file as part of the body of an email or as an attachment.
3. Word document. Many of you have been trained to submit Word documents for assignments for other classes, but these are not optimal for this class. It is difficult to extract images that have been embedded in Word documents for display on the web, and there is almost always a reduction in size or resolution as a consequence of this. In addition, text extracted from a Word document has character codes for some punctuation marks that must be edited to display correctly on the web.
4. Portable Document Format (PDF). You will be asked to submit a PDF of your final project report for Washington University, but this is the worst possible format for submitting day-to-day work during your annotation project. PDFs are a waste of memory on the class website and should only be used for class handouts or your final report.
5. Other formats. Some of the files that you need to submit for your final report will be in a very specific format (e.g. GFF) for use by our collaborators at Washington University. You will be shown how to do what you need to do in class, and the resulting files will be saved to the classroom hard drive.