Project work¶
Choose a project work. There are three projects to choose from:
- biological sequence analysis (part07)
- regression analysis on medical data (part08)
- fossil data analysis
The fossil data analysis project is currently not integrated to the TMC system, so for that, see the instructions from the tasks section of the course page.
For the two first projects (part07 and part08), download the exercises and/or notebooks from the TMC server. Then try to solve as many exercises as you can. Then submit your solutions to the TMC server. Note that the TMC server is only used here for helping you to proceed with the project work. Your final project work returned to Moodle can include partial solutions.
The projects differ a lot in their workflow. See the below sections on individual projects to see in detail how solving, testing and reporting of exercises are done in each project.
Save the report as a Jupyter notebook file (with ipynb extension)
and submit this file to Moodle. After this you will need to give feedback for your own
report and two other reports. See the tasks section of the course page for instructions on this peer-review process.
Sequence analysis¶
Download part 7 from tmc after you have completed the required number of part 6
as usual. The src-folder contain a jupyter notebook
project_notebook_sequence_analysis.ipynb. Run the notebook and fill in the
cells as instructed. You may run tmc test to see if the functions seem work as required.
The tests are not comprehensive, os a passing test may not imply a perfect solution, nor
does a failing test necessarily mean the there are critical errors.
Submitting may not work especially if you download content from the internet as
part of your code.
Next to each exercise in the report there are also two text boxes for you to fill. In the first box, in your own words, describe the idea of the solution to the exercise. In the second box analyse the results, including how the program worked with the given example input or your own examples. Make sure the notebook includes your solutions and looks readable, and then submit the resulting notebook to Moodle.
NOTE. Exercises in section “Stationary and equilibrium distributions (extra)” (exercises 20, 21, and 22) are not obligatory. Thus, you only need to do 19 exercises, if you are aiming to get full points.
Regression analysis¶
Read the introduction introduction-to-regression-analysis.pdf.
Note
It looks like the TMC server corrupted the pdf, you can read it from here
Write solutions to exercises directly into the cells of the given Jupyter notebook.
Do not modify lines that say # exercise x; without those the tests won’t work.
Don’t use additional cells, and do in each cell exactly as the instructions say.
Save the file and run tmc test. The tests read and execute directly the cells
of the notebook.
Make sure the notebook includes you solutions and looks readable,
and then submit the resulting notebook to Moodle.
Running tests when peer-reviewing students notebooks¶
If you want, you can run tests on the work you are reviewing, to help assess the correctness of the solutions. Note that there can be bugs in the tests too.
Warning
Make sure you don’t accidentally delete your own solutions, when testing other student’s work. Don’t do the tests where your own solutions are.
Regression analysis¶
Go to a temporary working area (like /tmp on Unix) so you don’t accidentally overwrite
your own solutions. Run tmc download -a hy-data-analysis-with-python-2020
to get the tests. Store student’s notebook to file
part08-e01_regression/src/project_notebook_regression_analysis.ipynb.
Run the tests using tmc test part08-e01_regression.
Sequence analysis¶
Go to a temporary working area (like /tmp on Unix) so you don’t accidentally overwrite
your own solutions. Run tmc download -a hy-data-analysis-with-python-2020
to get the tests. Overwrite the student’s notebook in part07-e01_sequence_analysis/src.
Run the tests using tmc test in the part07-e01_sequence_analysis folder.