MSc General

• We expect you to take the lead in your project. Your supervisors are here to advise and guide you, but it is up to you to manage your time, relationships, work, etc.
• BME MSc students now have some new excellent guidance documents with flowcharts available on the "Master Biomedical Engineering" Brightspace course under "ALL STUDENTS - Flowcharts & Guidance Docs". Please read these and reference them regularly.
• BMD & BME students are encouraged to join the "Graduation Community Program" for get togethers and workshops on topics to help you move through your MSc.
• BME and BMD MSc students now have some new excellent guidance documents with flowcharts available on the "Master Biomedical Engineering" and "Master Biomechanical Design" Brightspace courses under "Flowcharts & Guidance Docs". Please read these and reference them regularly. The guide here is a compliment to those documents.
• You are encouraged to join the "Graduation Community Program" for get togethers and workshops on topics to help you move through your MSc. This is especially helpful if you are struggling in your MSc.
• You have to write at least three documents for your MSc. Read the writing guide for tips and read the recommended papers below for even better tips!
• Review the Data Management Guide.
• If you are doing experiments, review the Experimentation Guide.

Internship

15 ECs (420 hours, ~10 weeks full time)

After you have found an internship, typically on your own but sometimes through postings via the lab, here are some things you need to do:

• Review the Study Guide explanation of your internship, for example:
  • BMD: https://studiegids.tudelft.nl/a101_displayCourse.do?course_id=59456
  • BME: https://studiegids.tudelft.nl/a101_displayCourse.do?course_id=59534
• Review the internship forms and guidelines (always use up-to-date forms): https://www.tudelft.nl/en/student/faculties/3me-student-portal/education/related/student-forms/internship-forms
• Fill out the MSc internship initiation form with your project description and other relevant information. Develop this project idea with your internship company/org contacts. If you think this aligns with Jason's research interests or the internship came through the bike lab you can send the form to Jason and ask him to be your TUD advisor. If he agrees, then you can obtain his signature on the form and forward it to your respective MSc coordinator.
• Make all of your internship arrangements yourself with the company (travel, stipend, housing, IP, NDA, etc.). Reach out to your TUD supervisor if you need help in any of these aspects.
• To receive academic credit for your internship at the end you need to write a report and have it assessed by your TUD internship supervisor. The short report should contain aspects aligned with those described in this rubric: https://wbmt2.tudelft.nl/organisatie/formulieren/msc/3me-msc-assessmentcriteria__internshipreport.pdf and the direction and needs of your external internship supervisor. This rubric will not be used to determine your grade, it is simply pass/fail based on the supervisor's review.
• You also need your external internship supervisor to fill out the form "INTERNSHIP ASSESSMENT FORM FOR EXTERNAL PARTIES" and submit the completed version to your TUD supervisor.
• Note that your TUD supervisor is typically not involved in your internship other than the signing the initial form and assessing and providing a grade at the end. The purpose of the internship is for you to get some non-academic experience in engineering. The internship should also be distinct from your MSc literature study and thesis project in the sense that a standalone report for the internship work is required.

Here are some companies and organizations that have hosted internships with us in the past: Gazelle, Prinoth, Garmin/Tacx, Swugo, B-Cells, Team DSM, SymPy, Bikefitting.com, TrueKinetix, velolab.de, TU Delft Sports Engineering Institute, Aalborg University Sports Sciences.

Literature Study

10 ECs (280 hours, ~7 weeks full time)

• If you are a BMD or BME student, read the relevant guidance docs found on Brightspace.
• Arrange an initial meeting with your supervisor(s) to discuss how to get started on the literature study and to discuss the general topic area of the study.
• Review the "MSc Literature Review Assessment Rubric" on the 3mE MSc Forms page.
• Read "How to read a paper" and "Ten Simple Rules for Writing a Literature Review" and review the "The Literature Review Process" website in the recommended reading section below.
• Choose and learn a tool/method to organize your papers and notes (e.g. Zotero, Mendeley, Endnote, Excel).
• The first goal is to read a large quantity of paper abstracts (phase 1 in "How to Read a Paper") to get a broad sense of what people are researching about the topics of interest.
• The second goal is to formulate a research question(s) that you can likely answer with the papers you read.
• Once you have a research question in mind, arrange a meeting with your supervisors to formally present the question and receive feedback (this should occur within the first two weeks of work). You should prepare a slide presentation or similar.
• The third goal is to delve deep into papers that are closely related to your research question, analyze and critique them, and synthesize the knowledge you obtain from them into a coherent answer to you research question.
• Before writing your report read "The Science of Scientific Writing" and "How to write a good (enough) report" in the recommend reading section below.
• Lastly, write up your findings for a technical audience in a way that answers your research question.
• Once you have a first full draft of the literature study, request feedback from your supervisors. This usually takes a week. You can arrange a meeting to receive verbal feedback also. Use the feedback to improve your document and then submit it to your supervisors for their official assessment and grade.
• As you approach the finish of your literature study you should schedule your colloquium, where you will present the results of your literature study to your peers. We encourage you to practice your colloquia with an ad hoc group from the lab or at a lab meeting. Send an invite to your colloquia to the lab.

MSc Thesis

35 ECs (980 hours, ~25 weeks full time)

Basic Steps:

• Submit MSc initiation form (BME/BMD form 4, other tracks may have a different form. You may do this at the start of your literature study, if appropriate.
• Formulate a research question or hypothesis that you'd like address in consultation with your supervisors (this usually occurs in the later portion of your literature study period and is informed by your literature study findings).
• Develop a written project plan (3 pages): research question/aim/goals, your basic technical approach, timeline, milestones, resources, etc.
• Organize a kickoff meeting with all of your supervisors to formally present your research project and project plan. This should be slide presentation or similar.
• Adjust your project plan based on the feedback at the kickoff meeting.
• Work on the project with your daily supervisor's guidance.
• Present your progress at a midterm meeting with all of your supervisors. The midterm should occur after you have significant preliminary results that demonstrate you can succeed in the final project execution.
• Work on the project with your daily supervisor's guidance.
• Once you are getting close to a draft thesis arrange a Go/No-Go meeting. This meeting should include all of your supervisors that will be on your defense committee. Typically give the supervisors one week to read and comment on the draft before the meeting. Prepare a (strictly) 10 minute slide presentation to get everyone up to speed at the beginning of the meeting.
• If you get a "Go" at the Go/No-Go meeting then you should initiate the arrangement of your defense by submitting the correct forms to your track coordinators and department secretaries.
• If you get a "No-Go", at the Go/No-Go meeting then take the supervisors' feedback and improve your work until you are ready for another Go/No-Go meeting.
• When you have a "Go", edit your thesis based on the supervisors' feedback. When you have a final version of your thesis, send it to your supervisors two weeks before the defense and submit it to the TU Delft Education Repository. Make sure to add an embargo if your work requires one.
• Follow the Data Management Guide and deliver your project assets to the lab principle investigator and any partner organizations.

Other:

• Always use up-to-date forms from here: https://www.tudelft.nl/en/student/faculties/3me%E2%80%90student%E2%80%90portal/education/related/student%E2%80%90forms/msc%E2%80%90forms/
• If your project is with a company or institution and/or requires transfer of sensitive information you will need to arrange the "Graduation Agreement at a Company" that abides by the TUD Graduation Conditions. You can find the forms here here: https://www.tudelft.nl/studenten/faculteiten/3me-studentenportal/onderwijs/gerelateerd/formulieren/msc-formulieren/. Discuss this with your supervisor(s) before you start.
• Read the articles about writing reports and theses in the recommended reading later in this guide.

AIO Weekly Emails

Lab members are expected to send out AIOs to their supervisor(s) and any project collaborators you meet with during your regular meetings if agreed upon with your supervisor.

"AIO" stands for Accomplishments, Issues, and Objectives. This email should contain three bullet lists:

• what you or your team accomplished in the previous week,
• what issues you encountered during that week and would like help with, and finally
• what your objectives are for the coming week.

The purpose of these are to share what you are doing with your daily supervisor and anyone involved in your project outside the lab. Some notes:

• If you are working in a team you can send out a single AIO for your team.
• The AIOs do not need to be elaborate, concise is best.
• No need to list your hours worked or who did what in teams.
• It is ok, and preferred, to reply-all if you want to comment on an AIO with a suggestion so everyone can learn and discuss.
• The AIOs are not a contest. Your supervisor is not collecting these to judge how much you accomplish, but they do care that you are working, attempting to make progress, and communicating with your lab members for help. If you had vacation that week or just didn't have much time to work, that's fine, just note that.
• If you need help via with issues, you need to provide enough detail for the reader to understand the problem.

The AIOs should be sent the day of your meeting with the supervisor. It can be before (we can use it as an agenda) or after if you prefer to work on the issues with me and then post outstanding ones and the revised objectives post meeting. Some students like to leave the objectives blank and add them after meeting with the supervisor. However you do it, each week the accomplishments should hopefully reflect the objectives you wrote the previous week.

Past Meeting Topics and Materials

Research Tools Contributions

Researcher have to use and develop a variety of tools to complete their work. For example, we will develop experimental equipment and software often in the lab. Many tools are potentially useful to other people inside and outside of the lab. Lab members should build on and contribute to the tools we use and develop in the lab. There is a general expectation to create and contribute to open source software and open hardware efforts while working in the lab.

Shared Cloud Space

We have a directory named "Fietslab Commons" on Google Drive. To access this, request that it be shared with you by your supervisor. This folder and it's contents should only be shared with other <netid>@g-tudelft.nl addresses that are members of the lab. <netid>@g-tudelft.nl is also the login username/email that you will need to use when logging into https://drive.google.com. Please avoid using the "Share" button to share with non-TUD accounts, until we determine best practices for this. Read and update the README files present in the Google Drive directories to learn how to use the space. If you create new directories, add a README file to explain what the purpose of the folder is. If you want to add large amounts of data (>10 Gb), inform your supervisor first because there may be a more appropriate long term storage solution for certain types of data.

Reference Management

The lab has a shared Zotero group which can be used for lab related reference management (currently 20 GB plan). Zotero is an open source reference management system backed by a consortium of libraries. Create an account and request membership to the mechmotum group. Note that all lab members can view the contents of this library.

Version Control

The lab currently has group accounts on Gitlab and Github for version control of text based sources (software, text, etc):

• https://gitlab.com/mechmotum
• https://github.com/mechmotum
• https://gitlab.tudelft.nl/bicyclelab

The services are more or less interchangeable. We used Gitlab in the past because it provided free unrestricted private repositories, but Github does now too. Gitlab's core software is open source. You may prefer the features of one service over the other.

Lab members should be able to make use of version control and communication through these services. The Software Carpentry Git lesson is a recommended introduction. Create an account on one or both services and request group membership.

Private repositories are private for a reason. If you gain access to private repositories in the two organizations you are expected to keep the private and not to distribute the files in any way. Ask your supervisors if you'd like to share something that is set to private.

Tidiness

• The lab should be kept clean and tidy.
• Place small trash into the two bins and paper into the blue box for pickup by the janitors.
• Place large trash, paper, cardboard outside in the bins near the bike cage. Do not leave this lying in the floor of the bike lab. It will not be picked up.
• Always leave the lab cleaner and tidier than you found it. If followed, this will tend towards a clean and tidy lab instead of the opposite.
• Always clean up before the end of a work day (reserve last 15 minutes to do so).
• Put items and tools back in their labeled locations. If there isn't a label or location, make one.

Safety

Our goal is to have ZERO injuries in the lab. Safety should be taken seriously and always prioritized. Some key things:

• Wear safety glasses and other appropriate personal protective equipment (PPE) when using tools. These are available in the lab or can be borrowed from the workshop. Contact your supervisor if we need more PPE.
• Do not use tools that you are not familiar with. Always ask someone to show you proper use.
• Any activities that have potential to cause injury performed outside of the 8:00-17:00 weekday (non-holiday) times should always have two people present. During the workday period it is recommended to have a buddy present when doing anything can cause injury, but the number of people in the halls and glass walls make this optional.
• The large treadmill always has to have two people for operation. When the treadmill is operating the walker/rider must be wearing the harness properly and the operator must have their hand on the kill switch. Ensure that objects cannot fly off the back of the treadmill.
• Human subject experiments must have an HREC plan and protocol (always for PhD, Postdoc and at minimum approval from your supervisors for MSc).
• If you are ever asking yourself "should I do this?", that's probably a good signal that you shouldn't. Get help, advice, training, etc. so that you do your activity safely.

Equipment & Consumables

If you find something in the lab you would like to use, post a note to the Element/matrix chat or lab email asking if anyone else is using it or plans to use it. If no one is using it, then you can!

If a TU Delft student or staff that is not a lab member would like to borrow equipment from the lab, find out if anyone is using it (as noted above), and then make sure they fill out the checkout sheet (by the lab door) with their name, email, date, and your name (as the responsible person) before the item leaves the lab. When they return the item, indicate the return date on the sheet. Keep in mind that non-lab member students should look to the more general shared equipment resources available in 3mE before borrowing from us and we don't generally loan common things like screwdrivers and bike pumps but can loan specialized equipment that only we have.

If you take things from the lab to use elsewhere for more than one day you also need to sign the equipment checkout sheet. Note your name and the date you took the item. Once the item is returned to the lab, note the date returned.

If you damage or lose equipment you are responsible for fixing or finding a replacement. Please let your supervisor know if this occurs so you all can figure out a solution. Your caution and carefulness should be proportionate to the cost of the lab equipment. Treat things as if they were your own and you paid for it.

If you deplete some consumables, take the responsibility to replenish it so it is there for future use.

Purchasing

If the lab needs basic office supplies or computer supplies, a request should be made to the secretary. Don't purchase these yourself, because they should be purchased through the university vendors.

If you need some lab supplies or equipment for your project, talk with your supervisor about it and they can order what you need if there are funds available.

TU Delft 3mE VAT number: NL 001569569B01

Equipment Inventory

When new equipment arrives in the lab, the receiver is responsible for inventorying the equipment. This only needs to be done for items that cost more than 250 EUR. The basic steps are:

• Log the equipment in the inventory spreadsheet on the shared Google Drive. This should include product name, manufacturer, serial number, manufacturer contact info, value, etc. (fill out the existing columns or make new ones if needed).
• Make a folder in the Google Drive for the product and deposit any documentation.
• If the item doesn't have a storage container, obtain one so that it can neatly be stored in the lab and things don't get lost. Leave paper documentation in the container.
• Permanently mark the item(s) and container with "TU Delft Bicycle Lab" (use a paint pen, inscribing tool, etc.)
• As you learn the device, leave any relevant documentation you obtain or create in the Google Drive folder so that future users can learn from your work. Include the manufacturer's documents as well as your personal tips and explanations on using the equipment. If any documentation is more appropriate for storing and tracking with version control, then add that to a lab owned Git repository.

Useful TU Delft MSc Courses

Multibody Dynamics B

Core high level dynamics principles that are the foundation for almost every project in the lab.

Special Topics Course in Sports Engineering

TU Delft organizes an annual two week course to train students in sports engineering. Cycling has been used as the motivating topic to learn the methods.

Musculoskeletal Modelling and Simulation (ME41005)

Learn how to develop and utilized computational neuromuscular models with OpenSim. Many projects in the lab make use of neuromuscular and biomechanical modeling.

Vehicle Dynamics and Control (RO47017)

Provides various fundamentals for understanding vehicle motion and how to control it. Focused on automobiles but many concepts transfer to single track vehicles.

System Identification and Parameter Estimation (ME41065)

We often make use system identification and parameter estimation for both vehicle and human control models.

Automatic Flight Control System Design (AE4301)

There are many similarities in single track vehicle control and aircraft control. This course also covers some topics on aircraft handling qualities which we make use of in understanding single track vehicle handling qualities.

Writing a Master's Thesis in English (TPM305A)

If you would like help and motivation on your writing assignments during your MSc, this course can be helpful to give structure, guidance, and others to discuss your thesis with.

The Carpentries Trainings

Each lab member will need to learn the collaborative software tools and open source development practices needed to work on code and other text based sources together. Carpentries trainings (Software Carpentry in particular) is a great way to get started on this. TU Delft offers regular courses:

• Software Carpentry Workshops

Sign up by emailing Femke van Giessen (F.vanGiessen@tudelft.nl) to register for a slot. You will be directed to an Evenbrite. Sign up on Eventbrite immediately because these typically fill up in 10 minutes and there are large wait lists.

• TU Delft Data Champions hosts events and trainings: https://www.tudelft.nl/en/library/current-topics/research-data-management/r/support/data-champions/
• 4TU Research Data Training and Events: https://data.4tu.nl/info/en/news-events/training-events/

Writing Help

TU Delft Writing Center

Schedule a meeting with a writing coach to get advice on your thesis or other documents.

Online

Biomech-L forum

A 30+ year old public discussion forum to connect to the international Biomechanics community. Lot's of great scientific discussions.

Single Track Vehicle Dynamics listserv

Public email based forum for discussing the dynamics and control of single track vehicles.

International Human Powered Vehicle Assocation

This group hosts the annual bicycle speed challenge in Battle Mountain Nevada.

World Human Powered Vehicle Assocation

Umbrella org for many associations around the world.

Ligfiets Vereniging

Dutch recumbent bicycle organization.

Software

R-Ladies Rotterdam

https://www.meetup.com/rladies-rotterdam/

Pythonistas-NL

https://www.meetup.com/Pythonistas-NL/

Conferences

PhDs and Postdocs should submit to and present at conferences each year, if possible. MSc and BSc students are also encouraged to do so if resources allow.

Bicycle and Motorcycle Dynamics Conference

This conference is the most closely related to the bicycle lab's core research in single track vehicle dynamics, handling, and control. The conference series ordinated with Arend Schwab and his colleagues and was launched in 2010 in Delft. The lab should make a strong effort every three years to submit to and be involved in this conference.

International Cycling Safety Conference

This is the next most important conference to be involved in. We should aim to have at least one or two submissions to this conference each year.

ECCOMAS Multibody Dynamics Conference

This is a good conference for presenting topics that focus in multibody dynamics methods.

International Sports Engineering Conference

This is the best conference to submit sports engineering topics. It is held every other year. There are likely many other TU Delft participants, especially through the Sports Engineering Institute.

International Society of Biomechanics Congresses

Huge annual conference with a broad array of biomechanics topics. Great networking and a catch all for many topics from the lab. Every two years. The Technical Group in Computer Simulation holds a parallel symposium.

SciPy & EuroSciPY

Annual conferences. If your work involves open source Python software these are a great place to showcase the advances in library development and use of the tools.

Dutch Bio-Medical Engineering Conference

Nice way to connect with Dutch local researchers.

Science & Cycling

Annual European conference focused on performance and cycling as a sport.

Introduction to Bicycle Science

David G. Wilson, Bicycling Science, 3rd ed. MIT Press, 2004.

Bicycling Science is the authoritative introduction text to the science and engineering of bicycles.

Edmund R. Burke, High-Tech Cycling, 2nd ed. Human Kinetics, 2003.

Science of competitive cycling.

Introduction to Bicycle Dynamics

K. J. Åström, R. E. Klein, and A. Lennartsson, "Bicycle dynamics and control: adapted bicycles for education and research," IEEE Control Systems Magazine, vol. 25, no. 4, pp. 26–47, Aug. 2005, https://doi.org/10.1109/MCS.2005.1499389.

IEEE control systems magazine article that introduces bicycle dynamics with a few different models and nice explanation of important control principles.

J. P. Meijaard, J. M. Papadopoulos, A. Ruina, and A. L. Schwab, "Linearized dynamics equations for the balance and steer of a bicycle: A benchmark and review," Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 463, no. 2084, pp. 1955–1982, Aug. 2007. https://doi.org/10.1098/rspa.2007.1857

Shows the fundamental bicycle model we typically start with for understanding lateral dynamics of single track vehicles. Introduces much of the important terminology and principles.

R. S. Sharp, "On the Stability and Control of the Bicycle," Applied Mechanics Reviews, vol. 61, no. 060803, Oct. 2008, https://doi.org/10.1115/1.2983014.

Robin Sharp developed one of the most widely cited motorcycle dynamics models in 1970 (also recommended read), but this paper is his take on bicycle dynamics, stability, and control after many years of work on the topic of single track vehicle dynamics. It also lays out a number of core principles for the study of lateral dynamics of bicycles.

Biomechanics

David A. Winter, Biomechanics and Motor Control of Human Movement. John Wiley & Sons, 2009.

The longtime best introductory textbook to biomechanics of human movement.

Awesome Biomechanics

Community curated collection of biomechanics resources with a focus on computational biomechanics.

Computing and Data

Software Carpentry Lessons

General introductions to scientific computing and best practices in reproducible computational science.

Scipy Lecture Notes

Nice, collaboratively developed, starting point for scientific computing with Python.

Hadley Wickham, "Tidy Data," Journal of Statistical Software, 2014, http://vita.had.co.nz/papers/tidy-data.pdf.

Lays out the idea of "tidy data" which is a tabular data format preferred and used by a large set of software.

Academia

Srinivasan Keshav, "How To Read A Paper," ACM SIGCOMM Computer Communication Review, vol. 37, no. 3, Jul. 2007.

Introduces a structured 3 phase method of reading scientific literature.

Ten Simple Rules for Writing a Literature Review, Philip E. Bourne, 2013, https://dx.doi.org/10.1371%2Fjournal.pcbi.1003149

High level tips for writing a literature review.

Engineering: The Literature Review Process https://libguides.asu.edu/engineeringlitreview/start

A guide from Arizone State University on writing and engineering literature review.

Writing a Scientific-Style Thesis: A Guide for Graduate Research Students, NUI Galway, Dr. Dermot Burns, 2017

A comprehensive guide to writing a thesis.

"The Science of Scientific Writing" by George D. Gopen and Judith A. Swan, 1990

Quick read that gives tips to improve your scientific writing style.

"How to write a good (enough) report by Andy Ruina

Prof. Ruina's pragmatic take on writing with a goal of clear communication of your ideas.

"ICMJE | Recommendations | Defining the Role of Authors and Contributors."

The International Committee of Medical Journal Editors created a basic guideline for determining who should be considered an author of an academic paper. This is a good starting point for making judgement calls on authorship and is what the lab will strive to follow.

"Academia Stack Exchange," https://academia.stackexchange.com/

A Q&A website about academia. You can find discussions on many useful topics and also participate in the discussions.

Open Science

Markowetz, F. Five selfish reasons to work reproducibly. Genome Biol 16, 274 (2015). https://doi.org/10.1186/s13059-015-0850-7

Five clear and compelling reasons for making your research reproducible.

Carpentries, "Good Enough Practices in Scientific Computing" https://carpentries-lab.github.io/good-enough-practices/

Lesson that gives the basics for dealing with data, software, and other digital artifacts of your science.

Other

Greg Wilson, "Meetings," The Third Bit, May 11, 2018. https://third-bit.com/2018/05/11/meetings/

Some nice simple guidelines for making meetings actually useful for the participants. There is a video and slide deck.