Introduction

According to course rules, biology students have 50% of the grade based on a project. Computer science students have an exam instead.

An ideal project uses several tools or databases to explore a single topic and explores these tools in some depth, e.g. by trying several options and comparing them. Try to understand how these tools work and what might be their limitations. These tools can be alternatives for the same task, subsequent steps in a longer analysis or separate analyses looking at different aspects of the same data.

You can explore the use of bioinformatics tools and databases relevant for your thesis topic, but you can also work on other topics of interest. You can work in pairs, but each student should focus more on a separate part of the project.

You will submit the final report as well as other documents/presentations as listed below to help you in the process. The deadlines and Moodle links are in the Tasks subpage.

Presentation guidelines

In the first three parts you submit a presentation in pdf format. Some general guidelines:

  • Always include your name and a title of your project.
  • This is a work-in-progress presentation, more similar to an informal team meeting than a formal presentation at a defense or conference.
  • However, help your audience by having all necessary information well-organized.
  • Do not try to add unnecessary formatting / graphics / effects etc. Figures showing important information are welcome, unnecessary clipart is not.
  • Use sufficient font size and color contrasts so that the presentation is visible on a projector.

Initial proposal

3% of the final grade

Choose a topic, submit 1 page presentation briefly explaing the background and general goals of your project. During the next tutorial for biologists, present this in 2 minutes and obtain feedback. At this point you can still change your topic based on the feedback or changed circumstances.

Extended proposal

8% of the final grade

Submit a pdf presentation with more details on your project plans. It should have 2 pages and it may contain optional supplementary pages with further details if relevant, but it is not guaranteed that you will have space to use these in the presentation. In addition to the background and goals, you should add a brief description of your data (what it is, how you will obtain it) and what bioinformatics methods you plan to try. Providing links to tools and databases is recommended. During the next tutorial for biologists, present this in 2 minutes and obtain feedback. After this point you need explicit permission from the instructors to change your topic.

Preliminary report

10% of the final grade

By this point you should have at least approximately 25% of your planned work finished and you should have clear plans for finishing the rest. The goal is to obtain feedback on your progress and plans.

Submit a brief pdf presentation to be presented in 5-10 minutes at a meeting of an instructor and several students. Describe the methods you used so far, what results you obtained, and what are your planned next steps. Mention any questions or problems you have; we will discuss these to help you with the final project.

It is not necessary to proceed strictly according to the plans presented at this point but you should not change the direction of your project too much without an explicit permission from the instructors.

Final report

30% of the final grade

Please submit a pdf with your project report. Below we list what should be included in your project, but it is not necessarily a structure of sections in the project. Specifically, you do not need to have separate sections for methods and results, but it is often easier (for both reader and writer) to interleave them, e.g. describe methods of one analysis and its results, then another analysis and so on. Cite sources relevant for your project.

Introduction

Give a background for your projects (what are your goals and motivation for choosing this topic, necessary biological background for understanding the project). However, it is not necessary to include a lengthy literature review.

Description of your data

Describe what data you used and how or where it was obtained. List its basic characteristics such as the length of the sequence(s), the number of sequences, from which organisms they come etc.

Description of bioinformatics methods

For each method or website, include the link to the server or link to the software download/description. If the method was not covered in the course, try to understand what it does and briefly describe it in your report. Describe what exactly you did (what data you used, what options you selected or were preselected) so that your analysis is reproducible by another person. Explain why you made these decisions or if you also tried other options. It is not necessary to document your work with step-by-step screenshots, but you can include a few screenshots if you think they are very important.

Results and discussion

Show the results of the analysis, usually as figures or tables. Discuss if the results are relevant for you and if they seem reliable or in agreement with other sources. If you tried multiple ways of doing similar analyses, describe their differences and what might be causing them.

Conclusion

In conclusion, summarize the main results and remaining challenges as well as what you learned and what was difficult for you on the project.

Final meeting

Several days after submitting the project, you will have a final meeting with an instructor to obtain final feedback and answer any questions. This meeting may influence the grade you get from your final report.