Guide


Contents

This page is intended to house documentation for lab members that describes the nuts and bolts of how the lab functions. It's primary purpose is for on-boarding new members, but is also a reference for current members. For this page to be useful, all lab members will need to provide their collective knowledge and experiences. It is up to all of us to make this guide useful. You are expected to contribute to the guide and edit it to do so. Discuss with the lab any desires to change any of the guidelines.

Getting Started

The Lab Community

  • Join the lab communication channels:
  • Send an introduction email to the lab email list (mechmotum@googlegroups.com): who you are, a bit about yourself, what you will work on, etc.
  • Add your name and portrait to the lab members page by sending a PNG or JPG 300px x 400px portrait to Jason or by submitting a pull request on Github.
  • Setup regular mentorship meetings with your mentor(s). This should at least be a weekly or biweekly depending on your needs and the mentor(s) recommendations.
  • Attend biweekly lab meetings. Ask a lab member for the calendar invite with the video chat link. Add your ideas and votes for meeting topics to the google document (ask Marco for permissions to edit).
  • Send out an AIO (see below) before your regular mentor meetings if requested by your supervisors.
  • Get campus card access to the bicycle lab and bicycle lab storage (if needed). These can be requested from Jason. Ask for a tour of the space from a current lab member before you start working there.
  • Request access to the lab's shared Google Drive.
  • See the recommended reading list below for some reading materials to get you started.

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.

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:
  • 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.

Literature Study

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

  • If you are a BME student, read the relevant guidance docs found on Brightspace "Biomedical Engineering Page".
  • 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 present the question and receive feedback (this should occur within the first two weeks of work).
  • 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.

MSc Thesis

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

Basic Steps:

  • (CoR based MSc tracks only) Submit MSc initiation form.
  • 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).
  • 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 present your research project and project plan.
  • 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 members of your defense committee. Typically give the supervisors one week to read and comment on the draft before 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.

Other:

COVID-Time Lab Rules

Use of the bicycle lab for hands-on project work is allowed as long as 3mE allows this type of work inside the building. Check with Jason for the up-to-date rules if in question. The current lab rules are:

  • All the University rules and 3mE rules apply and the following rules are in addition to those.
  • If you are sick, stay home and get tested. Let others you were in contact with know immediately of possible or confirmed COVID infection to prevent spread. Follow the Dutch government recommendations and regulations.
  • Take the virus seriously and respect everyone's health needs/wishes. Everyone should feel comfortable if using the space. Communication is key for this.

Communication

Lab Email List

When you join the lab you should request access to the lab email list:

https://groups.google.com/forum/#!forum/mechmotum

This can both be used by everyone as both an announcement list and a discussion list. All lab members need to join and pay attention to this list for announcements and are welcome to use if for discussion.

Text, Audio, Video Chat Room
We host a matrix server which can be accessed using https://element.io or any other supported clients. This is used for quick chats, meetings, etc. We'll keep the chat histories around, but its best to treat the data as transient. Lab members can use as needed for lab related communication.
Issue Trackers

We make heavy use of issue trackers on Github and Gitlab to communication. This is good for topic oriented, long form discussion that needs permanency, organization, and/or task control. General lab issues can be tracked in this repository (in addition to the website issues):

https://github.com/mechmotum/mechmotum.github.io

Quarterly Blog Posts
In general, we would like each project to write regular blog posts for the lab website. These posts should describe updates on project progress and results. This writing exercise will help build the content for future papers and theses and provide outreach to the public about our work. It is helpful to do these on a schedule (quarterly, semi-annually, etc.) so that the get done. If your project is of a proprietary nature, you'll need to select aspects of the project or work that can be shared or embargo the blog post to a later date. Discuss these things with your supervisor.

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.

"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.

Laboratory Meetings

We meet every two weeks as a lab, where we will have a designated person (picked in advance at random in our very own weighted raffle) take the proverbial stage and share and teach any topic that can be useful in our academic endeavors.

The topic can be anything bicycle or research related. It may be content-related, soft-skill related, practical-skill related or harking to your personal interest in bicycles. It might be an expertise or skill you have, but also be a skill or software program you want to learn. Co-presenting is fine (and a great way to meet your peers) provided your topics align. Options galore:

  • 10-20 minute presentation with Q & A
  • tutorial
  • have us read something (a paper) we could review (journal club)
  • watch and discuss a video
  • invite a speaker
  • play a game
  • practice your colloquia or conference talks
  • bicycle-themed stand-up
  • etc.

Members are expected to attend and participate regularly. It's fine to miss a meeting here and there, but avoid making that regular. If the meetings are not useful to you, please be proactive about helping us make them useful for all.

The MC position rotates approximately every quarter. See the MC Guide for instructions on being the MC.

Past Meeting Topics and Materials

Title Date Presenters Materials
Computationally Reproducible Papers 2022-01-18 Jason K. Moore Slides
  2021-12-07 Dorus de Boer  
  2021-11-09 Marco Reijne  
  2021-10-26 Jan Heinen  
  2021-10-12 Leila Alizadehsaravi  
Learning to stand with unexpected sensorimotor delays 2021-09-28 Patrick Forbes https://elifesciences.org/articles/65085
Robot bicycle overview 2021-09-28 Tim Huiskens Slides
Welcome back 2021 Q1, Browser-only Mechmotum website update 2021-09-14 Rado Dukalski  
Optimal Control in Biomechanics 2021-05-03 Joris Ravenhorst, Jan Groenhuis, and Jason Moore Slides
Balance and stability in elderly 2021-04-22 Leila Alizadehsaravi  
Introduction to Eline's Lab 2021-04-07 Eline de Kruk  
BioMechanical MSc Guide Review 2021-03-25 Eline van der Kruk, Jan Groenhuis, & Jason Moore  
Bicycle-rider perturbations & Bump’em 2021-03-11 Jelle Haasnoot & Shannon van de Velde  
Data Management 2021-02-11 Leila Alizadehsaravi & Rado Dukalski & Marco Reijne  
Bicycle Handling Qualities 2021-01-28 Julie van Vlerken & Jason Moore Slides
Bicycle Accidents and Crashes 2021-01-14 Joris Kuiper & Marco Reijne  
Bicycle Trainers 2020-12-17 Jelle Haasnoot & Rado Dukalski  
Introduction to Git and Github 2020-12-03 Tim Huiskens & Jason Moore Slides
BMX Racing 2020-11-19 Jan Groenhuis & Marco Reijne  
Introductory Meeting 2020-11-05 NA NA

Research Ideas

Specific MSc project advertisements can be found on the jobs.

Check out our research ideas Github repository to read, post, and discuss new ideas:

https://github.com/mechmotum/ideas/issues

Have a look at current and past projects on the research page

Open Science

The default science and engineering practice from the lab should be open practices (open access publications, open source software, open data, accessible and public sharing etc.). If unsure whether to make information public ask you supervisor, otherwise please default to sharing early and often. We do work with organizations that value or require privacy (human subject data, student protected data, proprietary company needs). Always check with the involved parties before sharing when this is the case. This is something that should be discussed at the beginning of all projects.

TU Delft offers several resources for open science:

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.

Lab Website

The lab website is a Pelican based static website hosted through Github pages. The source for the website is here:

https://github.com/mechmotum/mechmotum.github.io

Lab members should help collectively maintain and update the website. Please use the Github pull request mechanism to submit changes for review. As long as one lab member reviews the pull request and approves the changes, the changes can be merged. Keep in mind that content here should reflect the whole of the lab.

Software Tools

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):

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.

Lab Space

Using, removing, loaning 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, and date 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.

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.

Training

It is important to both learn the tools, methods, and techniques used in the lab and to teach the lab new things you've learned so we can collaborate efficiently and effectively.

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.

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:

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.

Writing Help

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

Connecting to Research Communities

We regularly participate in several research communities.

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.

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.
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.

Funding Opportunities

Dekker-Padget Internshiup Program: Dutch2USA
Funding for minority or economically disadvantaged college students to do an internship in the USA.
Veni
The Veni is part of the NWO's Talent Programme. It is the first of three personal grants. Postdocs in the lab that plan to continue in academia should apply for this. Final year PhDs are also encouraged to apply too. If you get this grant, you will gain a strong advantage in moving your academic career forward in the Netherlands. If you don't, you'll have practiced developing your personal research vision and goals, which is also extremely valuable.