TNW-PhD-Newsletters
Overview of the newsletters sent to the PhD candidates of TNW by the Data Steward. Below follow resources that have previously been sent out sorted on their main topic.
Data
Software
- TU Delft Resources
- TU Delft programming workshops
- See Coach View for future workshop dates and times
- TU Delft Digital Competence Center: Learn more about what type of data/code support the DCC offers on their website
- Code Refinery
- TU Delft R Cafés
- TU Delft Software Policy and guidelines
- Why a research software policy? The new workflow is an improvement as you don’t have to ask the Valorisation Center permission to publish your software through a disclosure form, as long as you follow the workflow.
- How to follow the workflow? A super concise summary is to share your code/software through 4TU.ResearchData choosing one of the TU Delft approved licenses (Apache, MIT, BSD, EUPL, AGPL, LGPL, GPL, CC0)
You can also choose another data repository, such as Zenodo, but then you have to ensure that the output is correctly registered in PURE yourself.)
- TU Delft has its own instance of GitLab meant particularly for sensitive data/code that cannot be shared externally.
If you have external collaborators in a project, GitHub is a better solution.
- How to get started?
- Workshop/Training materials
- Aalto University resources on making your computational workflow more reproducible
- Embrace the Command Line by using Jeroen Janssens’ book that is freely available.
- Licenses:
- Webinar: ‘How to set up a GitHub repository and your own website’
- document your code
- FAIR software recommendations
- Improving code readability
- Start with writing clean code by reading up on some blogs:
- Bugs: Check out how to avoid them and how to fix them.
- Software quality checklist
- For general software/data information, see the eScience Center guide and The Turing Way
- If sets, arrays and queues are not making any sense to you, you can watch this short video on data structures for a memorable explanation.
- Version Control
- You can check out a webinar on Practicals: Scientific software engineering principles, where the first talk focuses on version control and the last one on testing.
- For more resources on testing, check out another webinar on Software Testing in Open Source and Data Science (Eric Ma).
- ‘Science as Amateur Software Development’
- Learn how to improve your software management from The Good Research Code Handbook.
- Felienne Hermans wrote The Programmer’s Brain.
- [GitHub added built-in citation support]!
The only thing you have to do is create a CITATION.cff file in your repository, which will provide you with an example template that you can fill in in two minutes.
Link your GitHub repository to Zenodo or 4TU.ResearchData to make your software citable and add the DOI to the citation file!
- Sharing your code/software:
- The Turing Way now has a guide on Software Citation with CITATION.cff.
You can also go over this Software Citation Checklist for Authors.
- Software conference recordings
- Recordings of the ‘SeptembRSE’ sessions are available on YouTube.
See for example the workshop on software design and sustainability (starts at 8 min, with the more practical part at 1.20-2.14 and the coding/interactive part at the end), the discussion session on software testing, the panel on ‘missing narratives in discussions around diversity and inclusion in research software’, and a session on the different aspects of the RSE roles.
- FOSSY 2023 recordings are out!
This conference focused on the creation and impact of free and open source software has some interesting presentations on: Community lead user research and usability in Science and Research OSS: What we learned and Diamond Open Education.
- The CopyLeft conference from 2020 has some older but still relevant recordings on The Rising Ethical Storm In Open Source – Coraline Ada Ehmke and Collaborative Authorship Models in Open Source – Dashiell Renaud.
- The NORM conference has interesting talks on data visualistion, invisible work, file naming, Excel hotkeys, Docker, Data is the new coffee, and how to stop crying when using Matplotlib.
- Watch Margaret Mitchell’s PyCon2023 keynote on biases and ethics in machine learning.
- Distribits 2024: see the talk by Julia Thönnißen: Balancing Efficiency and Standardization for a Microscopic Image Repository on HPC, using tools such as datalad and rsync.
- Collaboration Workshops by the Software Sustainability Insitute recordings are available on their YouTube channel
- The videos of the 2020 Essential Open Source Software for Science conference are available on YouTube.
See for example the demo on Imaging & Microscopy.
- Open-Source Tools for Chemists workshop recordings are available on YouTube.
- It is important to document the dependencies and workflow for your software to allow others to reproduce your results (or for you to use your software on a different computer :)). You can list dependencies in a text file, or use more advanced tools:
- Python
- Sign up for Tony Hirst’s newsletter.
- Practical Python course
- Recordings from SciPy 2020
- See talk on Frictionless Data that introduces some tools to document your data more systematically and check your tabular data.
- The European Python Conference took place in July, and had some presentations on using Python to manage your projects: ‘Python table manners’ and ‘Scientific Python Cookiecutter’
- Python for Scientific Computing 2023: See the materials or specific videos on visualisation, data formats, productivity tools, dependencies, parallel computing, and packaging.
- ‘Data Science in Python beginner course’
- Use emojis in Python: pip install emoji.
- Python libraries: SMOP, a Matlab to Python compiler and spec2vec for mass spectrometry data.
- This presentation by Serena Bonaretti contains some nice resources (on slide 25, see https://doi.org/10.5281/zenodo.3939392) to learn how to use Python/Jupyter notebooks.
- Nbextensions seems handy for Jupyter notebooks (headers, notifications when cells are done running, code folding).
- Pylustrator offers an interactive interface to find the best way to present your data in a figure for publication. Added formatting an styling can be saved by automatically generated code.
- Learn more about testing your Python code by listening to a podcast on research software testing.
- PEP 657 tracebacks will annotate where exactly the error is happening in your code!
- Data Umbrella also has a monthly newsletters with events and tips focusing on Python.
Read their February edition and sign up!
- Check out the Python Cheat sheet by OpenAcademics
- course that introduces Machine Learning.
- Read the book ‘Python for data analysis’
- Or another book on ‘Research Software Engineering with Python’
- Check the course ‘Programming in Python for Data Science’
- This year’s JupyterCon videos are available on YouTube.
See for example the presentation by Franklin Koch on MyST Markdown: Using notebooks in scientific publishing workflows.
(You can also check out the Start using MyST Markdown in JupyterLab in 30 seconds video).
- PyCon AU 2023 recordings are available.
See for example Present like a pro! by Katie McLaughlin and Roll for Initiative: how to make the world of AI a more ethical place
- Checkout some Machine Learning Workshops (workshops descriptions)
- Read up on ‘Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks’ (Rule et al. 2019).
- Check out some options you have to check your Python code style.
- Get started with Sphinx improve your documentation practices.
- Or try out Python and Quarto to produce reproducible publications!
- And on a less serious note, listen to a 2 part ‘ interview’ with a Senior Python Developer: Part 1, Part 2.
- Read up on why you should make your Python code more modular.
- R
- Quarto
- Not sure what a Research Software Engineer is? Listen to Hello PhD podcast to learn more (7.40 – 40.00 for the interview with a Research Software Engineer).
- Need help picking a data notebook for your next project? Data Science Notebooks compares the features in different data science notebook tools.
- Check out this intermediate level crash course on management of software projects (for software that is beyond just an analysis script and is more a tool on itself!)
- Check if your repositories are included in Hugging Face’s The Stack.
Reproducibility
Open Methods
Open Science
- Open Science Community Delft
- TU Delft has an Open Science website.
- TU Delft’s Open Science online course
- TNW has an Open Science support website
- Open Life Science programmme (which TNW PhD candidates can follow for credits!)
No experience with Open Science practises yet? This Open Science Buffet poster will point you to some resources that we have at TU Delft that can support you!
- King’s Open Research Conference blogpost summary and recordings.
- Share your data/code on your CV! Check this example.
Make sure that you set up an ORCID so that you can always link to your ORCID in your CV!
- Check the Open Research Calendar or add its Google Calendar for Open Science related events!
- ‘Easing into Open Science’
- Open Scholarship Knowledge Base contains resources that can help you to make your research more open
- Watch this video on five things that you should know about Open Science
- Watch this video on how to become an Open Science Champion by Heidi Seibold.
- The Passport For Open Science is a guide for PhD students on Open Access, Data Management, and Reproducibility (click here to download the pdf directly).
(The authors are French but in general the resources will also be applicable to you, or there are TU Delft/Dutch alternatives available such as DMPonline - email me for more info!).
- To learn more about Open Access, read ‘A Researcher’s Guide to Open Access Publishing’.
- Read more about open and reproducible research in this blogpost/presentation by Laurent Gatto.
- ‘Food for Psychologists’ (applicable to any discipline working with data/code)
- The Open Science Framework released a recording of their quite practical webinar on ‘Leveraging Open Ecosystems to Enhance Reproducible Workflows’.
They demonstrate how to use the Open Science Framework in combination with Protocols.io, Python and R.
- RIOT has a YouTube channel on which they place recordings of their workshops and interesting talks.
- UNESCO released a short video on their Recommendations on Open Science.
- The PhD Talk podcast offers some pointers on “How we make our science more open”
- Watch a short video on “Open science for inclusive science” by Vittorio Saggiomo for TEDxWageningenUniversity
- Martijn Nagtegaal (ImPhys) attended the MRI Together Workshop in 2021 and wrote a blog about his experiences.
- Read more about the experiences of Anne Bülow, a PhD candidate at Erasmus University who was one of the winners of the Convergence Health and Technology Open Research Award in 2021, on her experiences with Open Science in the blog ‘Openess Opens Doors’.
One of the other winners of these Open Research Awards was Leila Iñigo de la Cruz from BN!
- The recording of the Open Hardware Summit 2022 is available!
You can watch it to get an idea of the (widespread) applications made possible by Open Hardware.
Highlights are the keynote by Ashley Jane Lewis (starting at 5.47) and the presentation by our own Open Hardware Engineer, Jerry de Vos (starting at 1:00:07).
- Watch a video by Cassandra Gould van Praag to learn more about how to get a DOI for your research outputs.
- Watch another video by Prof Stephen Curry on Open Research and DORA.
- To see how others started their Open Science journeys and get inspired, watch an interview with Dr. Malvika Sharan, or a recording of the eLife Ambassadors Open Science event.
- If you are trying to convince your supervisor that you want to share your research outputs more widely, Kowalczyk et al. 2022 wrote a paper on ‘What senior academic can do to support open research’. There’s also the ten-week plan for open data science that can be used as a starting point.
- What can you do to work more openly? Read this blogpost, especially the part by Dr. Mark C. Wilson who is offering some practical tips (scroll down a bit).
- Check out the Open Science Top Ten Tools!
- The US recently released an announcement that US funded research should be immediately accessible to the public, similar to policies that Dutch institutes and NWO already implemented.
Watch this short announcement video by Dr. Glaucomflecken.
- Checkout a video on Research Assessment at EMBL.
- Read up on why joining an Open Science community would be beneficial to you.
- Read how a PhD candidate learned how to embrace Open Science.
Open Education
Open Publishing
- Registered Reports
- Webinar: ‘How to get published and best practice for open research’
- SciPost
- Using Sci-Hub or Anna’s Archive to obtain access to paywalled articles is effective but actually illegal.
Please consider using the Unpaywall plugin for Firefox and Chrome to access these articles.
You can also check out a blogpost on Ten ways to find Open Access articles.
- eLife released a new article format: Executable Research Article.
This format allows for live code, data and interactive figures next to your manuscript.
- To avoid publishing with predatory publishers check out the checklists for books and journals from Think, check, submit.
- Short video on academic publishing.
- Video: introduction to Preregistration
- Watch two videos on the workings of the publishing system and article processing fees from Nature by Dr. Glaucomflecken.
- In related news, publishers now also tag PDFs with a unique hash, so you may want to be careful with how you share articles that are not Open Access (and publish Open Access where you can!), and remove the hashes where needed.
- A way to make the submitted version of your article openly accessible are preprints! If you haven’t heard about those yet, here are a couple of resources:
- Learn more about Open Access via keynotes and podcasts:
- Learn more about the recent Neuro Image editorial resignations from a video by Dr. Glaucomflecken or read up on how ‘How Scientific Publishers’ Extreme Fees Put Profit Over Progress’.
- Note that publishing Open Access does not have to be expensive – for example: SciPost and Peer Community In allow you to do this without costs to you. TU Delft also has deals with several journals which you can check in the journal browser.
- Read more about how to choose an open venue for your article.
- Learn more about how we’re going to get to ethical publishing from Fernando Racimo in a PCI Webinar.
- Watch a talk by Prof. Vincent Larivière on issues with academic publishing, open access and preprints.
- Watch a range of talks on what to do with the academic publishing system (particularly the first two talks and the last presentation), talking about the evolution of scholarly publishing, diamond open access (free to read and publish), and retaining academic publishing within our institutes.
- Learn about opening up the publication process by watching a talk by Monica Granados (28 -49 minutes in).
- Read up on why ‘Nature’ is prestigious or learn about the cost of Elsevier.
- Check-out an overview of mass resignations of editors from scholarly journals due to disagreement with publishers on Retraction Watch.
- Are academic publishers the original enshittificationists?
- Checkout a guidance document on Generative AI and Research Integrity by Mark Dingemanse from Radboud University.
- Read up on Self-Censorship and the Cult of Productivity in Academic Research.
- Johnny Coates asks: What’s wrong with academia?
- More is not better: the developing crisis of scientific publishing.
- Should you preprint your work? Read a case study about this, or some general motivations about Why you should preprint your next paper.
- Once you do preprint your work, Collaborative Peer Review Can Transform Scientific Research.
Open Science also increases the transparency of the review process, especially if combined with open peer review.
- Sharing is Caring: But How to Distribute Open Hardware?
- Negative results also deserve to be published!
- Transparancy in research also means transparency about positionality: Learn more about this from a Lightening Talk on Positionality Statements.
Preprints
(Open) Peer Review
Writing
Presentations and Posters
Copyright
Learn more about licenses for publications and data: Watch some short videos that:
Or read more about data licenses on The Turing Way.
Research Integrity
PhD things
- PhD Balance
- Scientist without a lab? PhD guide to COVID-19
- PhDForum Online Study Room
- TIGER in STEMM held a summer webinar series on physics research topics over the summer on YouTube
- Dutch Promovendi Network (PNN)
- “Strategies to overcome your challenges in multi-omics data integration’ materials.
- Blogpost on careers in data science
- Podcasts
- Blogpost has some tips on staying productive
- 12 min video on how luck plays a large role in success
- PhD on track website
- Resources
- Some points that you may want to discuss with your supervisor can be found in this Mentoring and Advising agreement document.
- This blog on managing your supervisor relationship contains some practical tips on time/boundary management that comes in handy not just with your supervisor but with anyone you’ll have to collaborate with.
- John Oliver’s Last week Tonight on Scientific Studies (from 2016)
- If you don’t know how a mathematical symbol is called you can draw it on the Detexify website that will provide you with potential names and LaTeX code!
- Are you losing confidence in yourself or your PhD project?
- Read this blogpost on ‘The Valley of Shit’ for some advice on how to deal with this.
- How do you know something (like your research, paper, dissertation) is good enough?
- Comic on Science Fictions
- Faking your daily commute
- ‘The Professor is in’ has webinars available to improve your productivity and a blog post on how to gain some motivation.
- For some more tips on how to get through your PhD you can read my blog “PhD in 4 - 5, 6, 7”.
- In case people are telling you to show more grit or just buckle up or work harder during your PhD, you might want to watch this video “Grittier Than You”.
- Prioritising
- In case you also manually scrolled back in an article every time you want to look up a reference in an article, you can use Alt + <- to return to the page you found it!
- If you then want to Get things Done: 1. Make a focus playlist, 2. Prepare, 3. Prioritize tasks, 4. Work in 90 minute sprints, 5. Batch similar tasks, 6. Eliminate distractions, 7. Relax afterward.
- Academia is not a calling – it is an “emailing”!
- Burn out
- PhD times can be tough! Be compassionate to yourself, and you can make it through.
- PNN has set up an overview of where to find support as a PhD candidate!
The PhD support compass allows you to find support such as the mentor program and PhD councils.
- Checkout the Grad Coach YouTube Channel for loads of videos on research related topics.
- Ten simple rules for how you can help make your lab a better place as a graduate student or postdoc.
- Failing is a key part of research – watch a talk about failures by Veronika Cheplygina.
- Listen to a podcast from PhD Talk on Supervision relationships, where they highlight that you should also discuss your progress in meetings with your supervisor, not just the content.
You don’t want to end up taking 7 years to finish your PhD!
- If you identify as nonbinary, join the International Society of Nonbinary Scientists.
- Read up on some considerations on letting go of authorship when moving to a position in industry after the PhD.
- Read up on Antidotes to cynicism creep in academia.
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- Read up on What Does Self-Care Really Mean?
- Read and learn How to restore work-life balance in academia.
- Learn more about giving feedback by using the Westerveld Framework.
- Read What examiners do: what thesis students should know.
Inclusion / Belonging
Career
- Chem4Word will allow you to draw different kinds of chemical reactions and specifying reactants, products, reaction type with reagents and conditions in Microsoft Word.
You can download the betaversion now and provide them with feedback!
- The Protein Data Bank in Europe (PDBe) and PDBe Knowledge Base (PDBe-KB) have tools available to analyse binding sites in protein structures (see the recordings of a webinar they hosted on this topic).
- For bioimage analysis needs visit forum.image.sc, or visit bio.tools for tools relevant to bioinformatics and life sciences.
Other