Useful resources throughout your PhD
Here is a list of resources that might be useful to you during your PhD.
Bioinformatics, Career planning, Deep learning, Funding opportunities , fu:stat, Github, Job application, Linear Algebra, Linux, Machine learning, Matlab, MAX, Mental health, Onboarding, Plagiarism detection tool, Poster, Professional figures and drawings, Project planing and time management, Python, R, Reading, Science communication, Scientific writing, Statistics
Feel free to suggest more ideas!
All employees and guests at the MPIGM have access to the MAX platform, the intranet of the Max Planck Society. To connect, select “MPI for Molecular Genetics” in the “Choose your institution” menu, and enter your personal number (you can find it on your salary sheet) and your password. If you are a guest, contact the HR office to get your personal number.
You can find more information on MAX here.
If you are struggling with problems that affect your mental health and well-being, don't stay without talking about it! You are not the only one and there is no shame in feeling down and asking for help. There are several solutions available to you:
- EMAP (Employee and manager assistance program) Life Coaching (MAX platform): Free immediate counselling services for employees and scholarship holders of the Max Planck Society, available 24/7, in German and English, if required Spanish, French, Dutch, Russian and Turkish, Call 0800-387 78 36 (Free of charge from the German landline network. Free telephone numbers from abroad can be found at www.fuerstenberg-institut.de https://www.fuerstenberg-institut.de/auslandsservicenummern/)
- You can contact the Student Association of the MPIMG.
- The Planck Academy (MAX platform) offers some webinars on Mental Health.
- The PhDNet usually organises a Mental Health Awarness Week each autumn and provides a lot of information: Read for instance the post Should I stay or should I go (out)? and the Immediate Help Document. More resources are available here.
Zoë J. Ayres, 2022, Managing your Mental Health during your PhD – A Survival Guide
You can take advantage of tools, coaching & training offers available to you at the Planck Academy (MAX platform).
You can access the inhouse Github here.
https://www.datacamp.com/courses/free-introduction-to-r
Nordmann et al., 2022, Data Visualization Using R for Researchers Who Do Not Use R (Paper and Bookdown for working through tutorial)
Altuna Akalin, 2020, Computational Genomics with R
Collauti, 2022, R Crash Course for Biologists
Books and courses about Python on O’REILLY
- Python http://mygreatlearning.com/academy/learn-for-free/courses/python-fundamentals-for-beginners
- Pandas http://kaggle.com/learn/pandas
- Numpy, scikit-learn http://simplilearn.com/learn-python-basics-free-course-skillup
- Data Science http://cognitiveclass.ai/courses/python-for-data-science
- Database http://freecodecamp.org/learn/scientific-computing-with-python/
- Data Visualization http://kaggle.com/learn/data-visualization; https://www.udemy.com/course/matplotlib-for-data-visualization-with-python-programming-language/?ranMID=39197&ranEAID=Vrr1tRSwXGM&ranSiteID=Vrr1tRSwXGM-bhM4qqOeI8X0NP8P5cdGGg&LSNPUBID=Vrr1tRSwXGM&utm_source=aff-campaign&utm_medium=udemyads
- Data Analysis http://openclassrooms.com/en/courses/2304731-learn-python-basics-for-data-analysis
- AI http://simplilearn.com/learn-ai-basics-skillup
- Machine Learning http://simplilearn.com/learn-machine-learning-algorithms-free-course-skillup
- Deep Learning (TensorFlow) http://kaggle.com/learn/intro-to-deep-learning
- Django https://openclassrooms.com/en/courses/6967196-create-a-web-application-with-django
- Flask https://www.mygreatlearning.com/academy/learn-for-free/courses/flask-python
- Design Pattern https://openclassrooms.com/en/courses/6900866-write-maintainable-python-code
- DSA https://www.mygreatlearning.com/academy/learn-for-free/courses/linked-list-in-python
- Testing openclassrooms.com/en/courses/7747411-test-your-python-project
- Debugging openclassrooms.com/en/courses/7744266-debug-your-python-project
The Linux Command Line, by William Shotts
The Max Planck Society has a licence with unlimited access to all online trainings and tools. You can find more information here: https://de.mathworks.com/academia/tah-portal/max-planck-gesellschaft-zur-foerderung-der-wissenschaften-ev-31194937.html. Click on “Sign in to get started” to create an account with your MPIMG email address.
Bioinformatics Algorithms: An Active Learning Approach by Compeau and Pevzner (textbook, free chapters here + videos):
MIT OpenCourseWare, Computational Biology: Genomes, Networks, Evolution, Health, Machine Learning in Genomics
Lectures and workshops at the Simons Institute for the Theory of Computing
HarvardX Biomedical Data Science Open Online Training: Data Analysis for the Life Sciences, Genomics Data Analysis, Using Python for Research
Applied Computational Genomics Course at the University of Utah
Introduction to Bioinformatics and Computational Biology by Shirley Liu
Data carpentry workshops on genomics
Computational Genomics: Applied Comparative Genomics by Michael Schatz
Introduction to Computational Biology by Mike Love (IMPRS-CBSC alumnus)
Self-taught education in Bioinformatics by Open Source Society University
Rosalind: platform for learning bioinformatics and programming through problem-solving
The Planck Academy offers a webinar on Improved Reading. You can find more details here.
Gosztyla, Nature, 2022, How to find, read and organize papers
Mensh & Kording, 2017, Ten simple rules for structuring papers.
https://www.coursera.org/learn/sciwrite
http://www.bushmanlab.org/assets/doc/ScientificWritingV39.pdf
https://cbc.arizona.edu/sites/cbc.arizona.edu/files/marc/Sci-Writing.pdf
Helmut Grubmüller, 2020, Scientific Writing: The Art of Programming Brains
Elisabeth Pain, 2023, How to write a research paper
Mireille Consalvey, 2023, A funding adviser’s guide to writing a great grant application
Users from the Max Planck Society have access to iThenticate, a plagiarism detection tool that applies text-matching algorithms to compare the full text of a given manuscript with a growing number of published scholarly works and web content. You can find more information here: https://ithenticate.mpdl.mpg.de.
All MPG employees have access to Biorender. Please check carefully the licensing terms beforehand.
How to create a better research poster in less time
Best tips on poster preparation, structure and content by Matthew Kraushar
Time to rethink the scientific CV, Nature 604, 203-205 (2022)
Tips for a successful CV for non-academic jobs
Tips for a successful cover letter for non-academic jobs
https://www.youtube.com/playlist?list=PLqPI2gxxYgMKN5AVcTajQ79BTV4BiFN_0
https://www.coursera.org/learn/machine-learning
Amidi & Amidi, 2018, Super VIP Cheatsheet: Machine Learning
Garrett Thomas, 2018, Mathematics for Machine Learning, University of California, Berkeley
Marc Peter Deisenroth, A. Aldo Faisal, Cheng Soon Ong, 2020, Mathematics for Machine Learning
fu:stat is the statistical consulting unit of the FU-Berlin, offering statistical consulting as well as statistical methods, software training and other resources. You can find more information here.
https://www.coursera.org/learn/stanford-statistics
ZEIT CAMPUS Ratgeber Promotion
ZEIT Campus Ratgeber Mental Health
Find the appropriate format for your target audience here.
Research funding portal of the Freie Universität Berlin
Federal Funding Advisory Service on Research and Innovation: They can help you identify a whole range of funding opportunities from various German government initiatives. They can also help you find local, national and EU research schemes, recommend partners, support international projects and much more. You can contact them by phone or email.
Research in Germany: you can find there funding opportunities for different career levels.
e-fellows.net awards fellowships to excellent students and doctoral candidates, including among others free access to German newspapers such as die Zeit, and Flixbus discount vouchers. You can apply here. The website is only in German.