Course Syllabus

Course Description

The Human Protein Atlas aims to visualize protein expression and protein distribution in all major organs and tissues of the human body. The laboratory of Jan Mulder at the Karolinska Institute is responsible for the brain section of the Human Protein Atlas, providing data on protein expression in various regions of the brain of different mammalian species. By using transcriptomics and antibody-based approaches to visualize protein location and transcriptomics approaches to detect protein expression, this research group aims to solve some of the biological mysteries related to (human) brain functions and brain diseases.

In our lab, we have generated very complex data with many layers and dimensions that cannot be captured in a single image. These include 3D volumed data on protein distribution in a tissue block that we currently share using Youtube. In collaboration with the startup Atomontage, we explored possibilities to share 3D data and to make this free, explorable, and interactive. As a research student on this project, you will get a raw 3D image set (stack of >1000 16-bit images) and use image processing tools (ImageJ, Matlab, or your favorite) and Atomontage webtools to generate a 3D model presenting the biological truth. You will then create tools and features to help/guide the users when exploring the data. Your principle mentor will be Jan Mulder, but you are also partnered with other bioinformatic researchers in the lab, the human protein atlas IT group, and developers at Atomontage.

Visualization projects: 

• Create an interactive 3D montage of biologial data based on volume imaging (mouse brain)
• Create an interactive 3D atlas of the human brain with links to data in the human protein atlas. 
• Create an interactive 3D representation of spatial transcriptomics data. 

Learning Objectives

Through the RA program, DIS students learn technical skills in a particular scientific field while experiencing the dynamics of a European research institution. Student progress is documented in a research journal and the completion of writing assignments (e.g. bibliographies, drafts, presentation materials, research papers) under the expertise of the Research Mentor. Student expectations may also include participation in group meetings, journal clubs, or other opportunities associated with active membership in a research laboratory. At the end of the semester, RAs share their work with peers and professionals in the Research Symposium at the DIS End-of-Semester Showcase.

As a research assistant on this project, you will decide on the type of data that you would like to work with. You will learn about this data (what it represents), how researchers use the data, and what they would like to extract when interacting with the data. Based on this evaluation you will set your aims and objectives and will identify tasks including 1) data processing (optimizing image data, segementation, etc), 2) creating a 3D montage in the cloud) and 3) create ways to interact with the data in the 3D world. 

Course Structure

The 6-credit RA experience is designed for highly motivated students with a strong interest in developing their research skills. Students must be willing to commit significant time during the term to hands-on research at an external local university or institute. Given the unpredictable nature of original research, time commitments may vary week-to-week; in general, students should arrange their schedules to dedicate an average of 20 hours per week to RA work, in close association with DIS and the Research Mentor. Specific hours and expectations will be shared by the mentor to ensure active participation in the research group.

An RA project is part of a larger, ongoing effort at a local research institution. Individual projects are student-motivated with the mentor's guidance and supervision. The goal is to pursue RA work of interest to the student, to their mentor, and to the larger research team. A gradual transition toward independence is encouraged, as the student gains confidence and is able to self-direct the work.

The primary product of the RA's work is an independent research paper summarizing literature and data reviewed, collected, analyzed, and contextualized by the student in the course of the term. Although it is not expected that the final paper be suitable for professional publication, it should document a clear rationale for the RA's work, appropriately referenced foundational literature, details of the approach and methods, preliminary results, and quantitative analysis, in support of subsequent phases of research in the larger group. The structure of the report should correspond to disciplinary standards, as specified below and in the rubric(s) provided.

Assignments & Evaluation

RAs complete incremental writing assignments to support their engagement and learning throughout the project, culminating in a final presentation and research paper. Evaluated assignments, and their contribution to the overall RA grade, are summarized below.

20 %  Presentation:  A live, short-form audio-visual summary of the semester's work, typically a poster or oral presentation, appropriate for an audience of DIS students, faculty, and other academics. By presenting the work shortly before completing the final report, the RA has a chance to finalize illustrations, plots, or other graphic support for their findings with the research mentor, and to discuss the project with a wide range of colleagues.

60 %  Research Paper:  Final written report of the student’s work throughout the semester, including project objectives, background context, approach/methods, data or other outcomes, analysis and significance to the field and the wider world. Although not produced with the intent of publishing, the final paper should be structured according to standards for primary literature in the field, and sufficiently detailed to support ongoing work in the research group. 

10 %  Participation Research assistant ship at KI:  A portion of the final evaluation based on attendance, citizenship, or other qualitative aspects of engagement as an RA. At the local institution, students are expected to maintain a research log and participate in meetings, journal clubs, and other opportunities as much as possible. At DIS, RAs also participate in workshops to support interdisciplinary reflection on the research process.

10 %  Participation Research community at DIS:  A portion of the final evaluation based on attendance, citizenship, or other qualitative aspects of engagement as an RA at DIS. These include particpation in research workshops and presentation of research at the DIS festival.

Mentors

Academic Regulations:

Please make sure to read the Academic Regulations on the DIS website. There you will find regulations on: 

• Course Enrollment and Grading
• Academic Expectations and Honor Code

Course Schedule

In addition to the key dates listed below and in the calendar, RAs are expected to communicate regularly with the Research Mentor. It is the student's responsibility to ask questions or seek additional support in a timely manner.

Before Arrival
RAs are connected with Research Mentors prior to the start of the term by email. Students may be provided 10–15 hours of preparatory reading material before the semester starts.

Weekly
When in Stockholm, unless otherwise arranged, RAs are expected at Biomedicum of the Karolinska instituted at the scheduled time-slots (individual schedules).