TP14_how_to_take_the_bioinformatics_test_on_your_own_computer\TP14_how_to_take_the_bioinformatics_test_on_your_own_computer
Instructions for computer test
This document was written to prepare you for taking the practical bioinformatics test. The test will be taken on your personal laptop or at a computer in the informatics lab.
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Make sure you have to have the software in the figures below working on your computer before the test. It is your own responsibility to install and test all needed software before the test. Note that the test is off-line, meaning there is no access to the internet during the test. This means you can typically not install from software sources on-line during the test. ApE can be installed from here.
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You need to have an MD5 checksum calculator installed on your computer. The MD5 checksum is similar in some ways to the SEGUID checksum, but in this case it is used for files.
If you are using you own Windows laptop, follow the instructions 2.1 , If you have a Mac, follow the instructions under 2.2. Finally, if you are using a computer in the CPII informatics lab, use the instructions under 2.3. If you are using Linux or if you have a Mac and know how to work on the command line, you do not need extra software, follow the instructions under 2.4.
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If you do not have Windows or you are using a computer in the computer lab, skip this step.
Get the “winMd5Sum.exe” from https://github.com/nullriver/winMd5Sum.
This file does not need installation.
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If you have a Mac you can use the command line to calculate the MD5 sum for a file. If you dont want tot do that you can install the MD5 software from here: https://md5.soft32.com. You should get a window similar to Fig 3.
There is a file in the same folder as this document :
md5testfile_should_give_md5_613f83bf6bae131a48d31667ef919242.txt
Question1: Verify the MD5 sum of the file above using your md5 software. To do this simply pull the file for your desktop to the calculator window. The md5 checksum should be 613f83bf6bae131a48d31667ef919242.
If you know how to work on the command line on your Mac, simply give the command “md5” followed by a space and the filename for which you want to calculate the md5 checksum. If you are using a Debian based Linux distribution such as Ubuntu, you can use the “md5sum” command like in Fig 4.
There is a Zip file in the folder of this document called Max_Maximus_99999.zip. This file contains an example test and other data files such as sequence files.
The password to unlock the file is “secret_password”.
🡇 Really important point 🡇
Use the given password to extract and save the test folder to the desktop of your computer (Fig 5).
If you start working on the test when it is still in the zip file, no changes will be saved.
🡅Really important point 🡅
Open the test file in Notepad (Bloco de Notas) or WordPad Fig 6 or another text editor of your choice. Do not use Microsoft Word.
The test text file contains a number of questions and placeholders (?) for your response in the form of question marks “?”. Fig 7 show and example question. Calculate the answer and replace the “?” with your answer as in Fig 8.
As you can see, the answer is given in correct FASTA format. This is required!
Sequences in different formats will not be understood by the correction software.
Do not modify anything else in the test file.
When you are done with the test, save it and use the MD5 software to calculate the MD5 check sum of your final test file.
Print a copy of the file “MD5form_for_electronic_tests_print_this_and_bring_to_test.pdf” and bring it to the test.
The only material needed and permitted is:
- The MD5form
- A pencil (lápis) + eraser
- A computer
Mobile phones, calculators etc. are not permitted. Communication during test is not permitted by any, means electronic or otherwise.
Hand in the filled in MD5 form. Upload your test file to blackboard. There is an item under “Content” or “Conteudo” that is called “BIOINFORMATICS TEST” (Fig 10).
Submit the text file as indicated in Fig 11.
Blackboard notes the hour of submission.
You have to submit your test *BEFORE* the deadline or your test will be ineligible.
ONLY If the blackboard upload fails, send the test file as attachment to: bjornjobb+test@gmail.com
Correction
The test usually have 6-8 different questions. Each question will be graded with points between 0-100. This value will be multiplied with a relative weight of each question. This relative weight is the “points” given for each question on the test (low for easy questions, higher for difficult ones).
The final score is your score / maximum possible score * 20, so final grade is 0-20.
Most of the grading is automatic. There will be a number of text files online called: question001_chk.txt, question002_chk.txt, question003_chk.txt etc., one file for each question in the test.
These files contain each question from each student with comments and grading. You can use this to check the correction of your test.
Question 2:
This is an individual question for each student. Follow this link that points to a Google Spreadsheet. You should find your name in the leftmost column. In the folder where you found this file, there is also a text file named with your name and student number like this:
Max_Maximus_99999.txt
Calculate the MD5 checksum for your file. Put the checksum in the spreadsheet under “MD5 of students file”.
See the example in the first row for “Max Maximus”.