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. If you're not a TNW/AS candidate you can sign up here: https://forms.gle/ieV5VcGcGbJNMwN89
- TU Delft resources
- DMPonline to set up a data management plan (see also the Research Data Management website for more information)
- TU Delft Research Data Management 101 course
- TNW/AS Research Data Management Policy
- Electronic Lab Notebooks: RSpace and eLABjournal are available for TU Delft researchers
- 4TU.ResearchData archive to share your data
- Project drive, SURFdrive or OneDrive to store your project’s research data - see storage solutions for a more comprehensive overview.
- Know Moore About Research Data Management (+ slides - Some resources mentioned in the webinar are Cambridge specific)
- The Turing Way also has a chapter on Research Data Management - and a lot more information on how to work more reproducible.
- Blogpost that contains some tips on how to organise your paperwork
- Webinar: Data licenses and management (1:04-1:17)
- Aalto University’s Introduction to Research Data Management
- Short video on file formats
- Organise your spreadsheet data with OpenRefine/Frictionlessdata/Excelint (see also this lesson on OpenRefine by the Carpentries).
- ROpenSci webinar “The Wild World of Data Repositories”
- Learn more about Data Management Plans (DMP) by watching a video on DMPs
- file naming
- Have a look at this presentation on naming things or a blogpost on how to make your files more findable.
- Improve your file naming practises by watching a 5 min video
- Want to rename multiple files? The Bulk Rename Utility may save you a lot of time (but be careful with overwriting things)! This short data organisation/documentation manual can help you with file naming but also folder organisation.
- Suffering from messy datasets? The ultimate guide to data cleaning contains some tips to clean it up! See also these slides on the Practicalities of Data Handling and a blog on Tidy Data with nice illustrations.
- Learn more about how to organise your research project through this short video.
- Setting up your readme file has never been easier with the readme.so online editor.
- When you use arXiv you can now link your publication to a dataset! arXiv now also asigns DOIs!
- There’s a materials research data alliance community: www.marda-alliance.org.
- organising files
- The ‘Quick Guide to Organizing Computational Biology Projects’ is relevant to all research projects and also goes into a bit more detail on how to organise your files.
- Read a blogpost on ‘How to Organize Your Digital Files’.
- Learn how to manage your project, folders and files from this short video series on Project Structure by Danielle Navarro (see here for the slides).
- Prevent having to save your data from extinction by reading about a data ecology horror
- If you’re working with survey data – generate a data dictionary!
- Check the slides or recording of a talk by Ten Common Data Management Mistakes by Crystal Lewis
- Checkout a helpful overview of data visualisation resources
- Data Sharing
- This blogpost ‘How can you make research data accessible’ describes five steps that you can take.
- Wellcome’s (UK funder) data sharing guide (pdf) provides a short overview of things you will encounter if you want to share your data and contains a lot of good resources that help you to get started!
- Publishing and citing data in practice - ~30 min YouTube webinar
- 5 ways sharing your research data could help enhance your career – Nature blogpost
- CODATA webinar on sharing your data with your publication
- How to cite data in your paper by Esther
- Once you share your data you need a Data Availability Statement in your article. See these tips from Springer Nature for writing this statement.
- Webinar on transparency and qualitative data sharing
- Learn more about how to share your research from PLOS
- Sharing biological data: why, when, and how by Wilson et al. 2021 provides some pointers on how you can share biological data, specifically tabular data, genomics, proteomics, microscopy, and structural biological data.
- Read a publication on the application of the FAIR principles to materials research
- Watch a webinar on data/software sharing guidance.
- Personal Data
- Personal data is any data that can lead to the identification of a person. If you work with surveys, interviews or videos of people – you’re working with personal data. This requires extra care when managing the data. See for example the data privacy strategies outlined by The Turing Way.
- TU Delft now has a self-paced personal data course. You can sign up and follow it for 0.5 GS credits. See the website for more information.
- If you want to learn more about the laws that regulate processing of personal data, such as the GDPR, you can watch a talk on ‘GDPR & processing of (identifiable) image, audio, and video data’ or ‘Putting Data Protection into practice’ (18:30-38:50). Or if you’re working with any clinical data: ‘Open Data and Data Management in Clinical Research’.
- 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.
- TU Delft programming workshops
- How to get started?
- Workshop/Training materials
- The eScienceCenter is now sending out newsletters so that you can keep up to date with the workshops that they organise: sign up here.
- ‘Intermediate Research Software Development in Python’ course in your own time as all the materials are available online/on GitHub.
- Binder workshop materials
- RIOT: Version control for academics with GitHub, Dr Sam Forbes
- Follow an introduction to version control with GitLab by Dr Cassandra Gould van Praag.
- Writing Reusable and Modular Code.
- Learn more about Computer Science.
- See also this List of Free Learning Resources In Many Languages
- Aalto University resources on making your computational workflow more reproducible
- Embrace the Command Line by using Jeroen Janssens' book that is freely available.
- Licenses:
- website with explanations on licenses in plain English
- choose a License website (TU Delft recommends MIT license for software)
- See what TU Delft requires from you in terms of Open Source Software.
- Learn more about software licencing via a FAQ or a podcast by ByteSized.
- Webinar on Open Software licenses, where they also discuss readme files (30.48 – 41:00), which you need for your project to describe it to others and tell them how to interact with your code/software. You can also learn about contribution guidelines and how to set up a code of conduct (46:00 – 1:01) from the same webinar.
- Webinar: 'How to set up a GitHub repository and your own website'
- document your code
- FAIR software recommendations
- Improving code readability
- Slides (.pdf) on Writing clear code by Karl Broman
- Presentation on Code Smells and Feels by Jenny Bryan
- Slides on Writing Clean Scientific Software by Nicolas Murphy
- Example video of how to structure your code by Anton Akhmerov
- Slides with 15 tips to write better analytic code by Francisco Rodriguez-Sanchez
- Read up on Why comment your code as little (and as well) as possible.
- 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
- Software Sustainability Institute checklist (it is a google form)
- Core Infrastructure Initiative
- EURISE guide
- 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
- Blog on Git or Perish
- Learn more about version control in this blogpost on Why mycode.R_final.v2_usethisone is not helping your workflow.
- If you want to work more collaboratively using version control you can consider using GitHub or TU Delft GitLab. TU Delft GitLab is intended for private/secure repositories, whereas GitHub is easier to use if you do not work with sensitive code and need to collaborate with externals.
- Learn more about Git and GitHub via Perez-Riverol et al. 2016
- You can generate the text for your GitHub profile using profilinator or the GitHub Profile Readme Generator
- You can also implement GitHub Actions to check for errors in your data processing and cleaning: see Kim et al. 2022 for more details.
- 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:
- Need some more help on how to make your project publicly available? Watch this short video by Dr. Barbara Vreede on sharing your project.
- Doubting whether your software is ready to be published in the Journal of Open Source Software? Read a blogpost about to know for sure.
- Sharing brain MRI data/code
- Vlog on how to start with code sharing.
- Why share your code? Read some reflections from the social sciences that are widely applicable.
- Top ten reasons to not share your code (and why you should anyway)
- Krafczyk et al. 2021 share some helpful recommendations on how you can share your software (pages 5-11).
- Read up on reproducible and FAIR software via a blogpost by Peter Kalverla.
- GitHub is a great platform to share software but it won’t preserve your code for the long term (for example, GitHub changed github.com to github.io, resulting in a lot of broken links). Instead, you can preserve a snapshot of your code on either Zenodo or 4TU.ResearchData (Connecting your GitHub/GitLab account).
- Best Practices for Writing Reproducible Code by Utrecht University!
- The Research Data Management 101 course had some additions for software sharing.
- You may be asked to share your code by peer reviewers!
- Read this blogpost on how peer review of software can improve the quality of your work
- Learn more about code review in a webinar by Lisa DeBruine
- You can also use notebooksharing to share your Jupyter and R Markdown notebooks with co-authors.
- The Journal of Open Source Education publishes open-source educational materials and 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.
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Open-Source Tools for Chemists workshop recordings are available on YouTube.
- See for example: DataWarrior; PyMOL; GoogleCoLab; CheMBL; Fragalysis; Knime
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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:
- Conda (Python) or renv (R): a package/environment management system.
- myBinder: online service to make your repositories interactive and executable.
- Docker: containerisation platform that allows you to package, distribute, and reproduce software and experiments in a consistent and portable way.
- Snakemake: workflow management system for creating and executing reproducible data analysis pipelines (Mölder et al. 2021).
- See also Secrets and environments to prevent accidental sharing of information!
- How can software containers help your research?
- learn more about software containers.
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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
- Delft RCafe resources
- UseR! 2020 presentations are available on the useR! YouTube channel - how to make your paper/code more reproducible by Anna Krystalli (see slides and materials) - use the here package to make it easier for others to work with your code (see this video) - see GitHub to work collaboratively with others using version control, and use the renv and drake packages (see this video)
- Open R Stream
- Short podcast on using Git/GitHub (and R), with nice resources to get started
- 15 minute video on the R Package WORCS, Workflow for Open Reproducible Code in Science (WORCS)
- ‘R for Excel users’ course
- Read a blogpost on Beautiful Code, Because We’re Worth It
-
Quarto
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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).
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Need help picking a data notebook for your next project? Data Science Notebooks compares the features in different data science notebook tools.
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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!)
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Check if your repositories are included in Hugging Face’s The Stack.
- Read a chapter about ‘Reproducible Bioinformatics Research for Biologists’ (for anyone with more wetlab experience than programming!)
- Follow a reproducibility checklist (pdf) set up by NeurIPS.
- Check out slides by Jason K. Moore on computational reproducible papers.
- Watch some videos/seminars:
- ‘Towards a Culture of Computational Reproducibility’
- ‘Steps towards reproducible research’
- How to make your research reproducible? (requires you to register to watch on demand)
- videos on how to do open and reproducible research
- Approaches to Scientific Error with Dr. Amy Orben
- Why openness and reproducibility makes research software better by Yo Yehudi
- Data sharing and reproducibility by Dr Laurence Hunt (you can use 4TU.ResearchData and/or Zenodo to share data publicly!)
- Open and Reproducible Coding: Perspective of an MSK Imaging Researcher by Serena Bonaretti
- Improve your workflow for reproducible science with a focus on rMarkdown by Mine Çetinkaya-Rundel
- Improving openness and reproducibility of research by Brian Nosek
- Ensuring your work is reproducible can prevent retractions later on, particularly when there are software problems.
- Does condensed matter physics need to worry about a replication crisis?
- Slides on Data Management and Reproducibility: A Tasting Buffet by Shern Tee.
- Docker is a tool for reproducibility and portability. Learn more about Docker and how can you start using it.
- Podcast episode ‘Reproducible data science, how hard can it be?’
- Best practices for writing reproducible code (slides by Barbara Vreede)
- Lisa deBruine has written a short guide for authors that want to share their code in a computationally reproducible way.
- Read a blogpost on Keeping science reproducible in a world of custom code and data
- Physical samples also play a role in reproducibility: Organize your –80 °C freezer to save time and prevent frozen fingertips.
- Check out community-developed checklists for publishing images and image analyses by Schmied et al. 2023.
- Try out Surge: a fast open-source chemical graph generator!
- PLOS ONE introduced two new publication formats: Lab Protocols and Study Protocols!
- Did your recent experiment fail? Read a blogpost on negative results. Note that you can still publish on these experiments through journals such as the Journal of Trial and Error and Experimental Results.
- You can also share your methods through platforms such as protocols.io. See this feature on ‘Five keys to writing a reproducible lab protocol’ for some pointers.
- Read up on the possibilities for providing access to reagents.
- Watch a video on how to write a reusable, step-by-step protocol
- 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.
- Registered Reports
- Webinar: 'How to get published and best practice for open research'
- SciPost
- Using Sci-Hub 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.
- 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:
- On Preprints
- eLife now only reviews and publishes articles that are shared as a preprint. Read more about how this works in their guide for authors
- Having doubts about posting a preprint? Read a blogpost about experiences with sharing a first preprint or "Why do some researchers have reservations about preprints?"
- Or watch Preprints: A Practical Guide
- Learn more about Open Access via keynotes and podcasts:
- Locked up science by Claudia Frick.
- April Hathcock's keynote on Open Access.
- The Labors in Ohr podcast introduces the History of scientific publishing with a follow up on Open Access with Bjorn Brembs and an episode focused on Plan S.
- 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 crash course in the history of publishing and sharing your research through a preprint as an act of resistance to the publication pressures.
- Learn all about preprints from Jessica Polka or check a webinar on 'How to Publish Preprints'.
- Not convinced about preprints? Check out a video on How preprints can benefit both science and your career or read a guide to preprinting for early-career researchers that lists benefits and arguments to convince co-authors to preprint.
- The Turing Way has a chapter on Peer Review, including a section on Open Peer Review.
- Listen to some tips to manage peer review (also check out the episode on how to publish a paper).
- To suggest peer reviewers to the editor/journal, remember when other researchers interacted with you (meetings, conferences). Write their names down somewhere (a reviewers.txt file). Or check which articles/authors you're citing!
- How do you respond to a review? EASE provides a 6 step guide and Dan Quintana wrote a short blog about this.
- Watch a panel on ‘Discussion on Peer Review: "Thinking With” When Peer Reviewing’.
- Check the Open Reviewers Review Guide. Pages 28-31 provide insights about what a reviewer would look for when evaluating your manuscript.
- Read some reflections on reviewing in the publishing system.
- TU Delft Library organised an event on Peer review: Peer Review under Pressure: how do we ensure research publications are of high quality? Watch the recording to discover more!
- Read up on The rise and fall of peer review.
- Listen to Chris Chambers discussing new forms of publication and revision.
- Read up on how to write concisely for any writing, including peer reviews.
- The PubReCheck tool can identify some issues with your text
- 11 step guide to structure your paper
- How to write a literature review
- Manage your reference with Zotero. Zotero allows you to annotate pdf’s and extract those annotations! See also How Zotero can make your writing life easier.
- Use Recite to check your citations
- If you’re stuck with writing, this webinar on “the art of productivity” might help you to get unstuck. In sum: You should be realistic about your expectations, block time for writing and stick to it!
- Grogan (2020)’s “Writing Science: What makes scientific writing hard and how to make it easier”
- Draftable allows you to compare pdf’s (in case you want to go over the pdf proofs of a paper).
- SciTLDR: a tool that summarises papers in one sentence!
- Brief guide to writing manuscripts (with benefits of Open Science listed on page 6)
- How to write a great science paper – tips from a novelist
- Watch a short video on how to write an abstract
- Follow this Coursera course on ‘Writing in the Sciences’ to improve your writing skills. Particularly week 1-4 contain important information on how to structure your article and improve your writing.
- Writing your first article? This two-page article contains a good set up for your introduction and questions that you should address in your discussion (it is a bit medical focused but mostly generally applicable). This blogpost also shows you how to structure your article.
- How to write an abstractfocusing on five sentences :
- What we know from the current literature.
- What we don't know from the current literature.
- What we did in the current study to address sentence 2.
- What the findings from teh current study are.
- What the implications of the findings from the current study are.
- Answer the questions below in your introduction or watch a video:
- Importance - Why is your field important? Why should a reader read your paper?
- Background - What does your reader need to know about your topics to understand your results?
- Problem - Why is your research important? What problem does your research solve?
- Context - How have you and others researched this problem? What articles led to your research?
- The five ingredients for a successful methods section.
- TU Delft offers access to the ‘academic writing assistant’ tool that can help you to improve the structure, style and spelling of your text.
- ‘How to navigate authorship of scientific manuscripts’ (you can use the CRediT roles to track contributions to the work, and use Tenzing to easily record these roles). You may also want to read: ‘Why scientific journal authorship practices make no sense et al.’
- Watch a RIOT talk on ‘Reimagining scientific publishing’
- The HemingWay Editor allows you to check if your sentences are written clearly.
- Lex is a new word processor with AI assistance to help you to write.
Learn more about licenses for publications and data: Watch some short videos that:
- Provide insights into the copyright agreement signing during the publishing process.
- Introduce licenses.
- Go over the different types of Creative Commons licenses (see the license selector to choose your own data license).
Or read more about data licenses on The Turing Way.
- Read PNAS is Not a Good Journal or check out this Elsevier comic.
- Learn more about research integrity via webinars and conference recordings:
- Recordings of the National Symposium on Research Integrity 2020
- Trust: What does it mean and how can we build it?
- The UK Research Integrity Office (UKRIO) hosts regular webinars on Research Integrity with recordings available on YouTube.
- What is Research Integrity?
- Sexual harassment and assault in Astronomy and Physics
- Research Integrity @ MTU recordings
- Addressing Global Power Asymmetries through Responsible Research
- Read up on how a Prominent nanoscientist retracts paper after PhD students flagged error
- Listen to podcasts on research integrity:
- Ensure your citation practices are more inclusive!
- The FEM/UM Citation Guide explains how women and other underrepresented groups can become more visible in science through citation practices.
- Balanced citer allow you to perform statistical analyses using Python to investigate the equality in gender and race of the first and last authors in your reference list.
- Watch a 10-minute mini-module on diversifying citations (the mini-module starts at 1:00:20). You'll also learn about positionality statements!
- PhD Balance
- standing up for yourself
- adapting to change
- Academic Mental Health with Zoë Ayres
- 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
- Read Alexandra Lautarescu’s blogpost on the tools she is using during her PhD or Sam Westwood’s blogpost on ‘Time-saving things that actually work’
- Overviews of tools by Achintya Rao and Helena Hartmann
- Use the Early Career Research Central to find and discuss opportunities, and share experiences
- PhD Kickstarter, FAQs to help you start and manage your PhD
- 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
- The Guide to Saying No (starts at 9:30)
- Not overextending ourselves
- Use one of the 20 templates to say no to turn down any opportunities/requests that you don't have time for.
- 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.
- Tatiana Mac’s White Guyde to the Galaxy and Save the Tears: White Woman's Guide
- documentary ‘The Uprising’
- If you saw no problem with the recent Safra et al. paper about trustworthiness of facial cues, you should have a look at this preprint (arXiv:2009.14258) by Birhane and Guest.
- Podcast: How to dismantle systemic racism in science
- webinar on inclusion organised by eLife
- ‘Picture a scientist’ documentary (that you can watch if you’re logged in through the TU Delft network!)
- Diversity and Inclusion in Research, Technology and Design
- Slack panel on Trailblazing women in tech.
- Susanne Täuber was fired this month for writing an article on her own experiences to write a critique of the system, showcasing how programmes that are intended to help women can actually get in their way. You can read more about the case and how to support Susanne, listen to a podcast, or use #AmINext to find posts about this on social media.
- Preprint highlighting the gender inequality in ‘cum laude’ for PhD candidates at a Dutch University, where women were ‘almost two times less likely to get a ‘cum laude’ distinction’.
- Article on how well intent alone does not address inequity in STEM.
- Not everyone will become a PI after their PhD, or wants to become one!
- Career outside of academia
- List of postdoctoral fellowships set up by the Johns Hopkins University
- Browse a collection on postdoc fellowships in biology.
- Want to stay in Dutch Academia? Read Eva Lantsoght’s blogpost on 'Diversifying career paths in the Dutch universities'. Eva mentions finding your strengths, which the StrengthsFinder website can help you with!
- Structure your CV
- You can use your ORCID to generate a CV (with R).
- Generate your CV easily using a template.
- Writing grants
- The Open Grants repository contains grant applications that got funded or rejected that can serve as an example.
- Hsu et al. 2021 contains short interviews with people in academic hiring committees (pages 9-11) that provides some insights in the hiring process (publications/funding may be less important if you have a clear vision on your work and are able to communicate your research well!). While the data is based on neuroscientists, some of the things are more generally applicable (such as institutions showing a preference for hiring individuals that they know).
- Browse through an overview of successful grant applications and interviews.
- Not sure what to do after your PhD?
- This interview with Jennifer Polk contains some helpful pointers.
- Listen a podcast on career uncertainty.
- Do a job search and find 25 jobs that you find interesting. Copy the requirements and group them: focus developing the skills in the top 3-5 mentioned requirements/skills.
- Read a blog by ERClife on “Early Career Researchers, take charge and develop your career” or by Lizzie Gadd on “Five steps to healthy research career building”.
- When you get invited to a job interview, come with questions!
- Read a blog by Anthony Disney, or the HBR article by Amy Gallo for inspiration.
- See also 6 things to say during job interviews.
- There is an AltAcChats podcast where you can learn more about Alt Academic career paths.
- Do you suffer from networking anxiety? This Infographic by PhD Balancing has some tips!
- Read up on salary information in Europe: Uncompetitive pay is behind exodus of academics in Italy.
- Read some Tips for Early Career Academics.
- Read a postdoc's experience on redefining academic success.
- 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.
- In case you want to know what data Elsevier collects from you, read the blogpost ‘Welcome to Hotel Elsevier: you can check-out any time you like … not!
- Mastodon
- elilla wrote a comprehensive Mastodon introduction
- blog by Danielle Navarro
- How to Join Mastodon blogpost
- blogpost by Stammy
- SURF also hosts a pilot which is making it easy to join their instance and get started!
- If you haven’t wrapped your head around Mastodon yet, use the Mastodon Quick Start Guide to get started!
- machine/deep learning
- Sign up for a machine learning newsletter.
- Read about five ways deep learning has transformed image analysis, also with the help of Citizen Science!
- Check out visual explanations of machine learning concepts.