Resources

Table of ContentsIISER Pune Biology Course Notes PhD Application Research Project Organisation Offering Feedback and Guidance Miscellaneous

IISER Pune Biology Course Notes

This page contains relevant information about the notes compiled by Vasudha Kulkarni (Batch 2019-24). The notes are scanned versions of handwritten notes for mostly elective biology courses credited over 2nd year to 4th year at IISER Pune. The information regarding the year and instructors is given in the table below.

DISCLAIMER : The notes were made during or after class and certainly don’t claim to be complete or sufficient in any regard. I’m sharing my notes in the spirit of open science, and I hope they might be of some use to other people taking the same courses. Please ignore the occasional bad writing, grammatical errors, and frustrated comments in the margin. Sorry for some blurry pages or lines – you can contact me if you need it explained, but I’m not sure how much help I would be. Any mistake in the notes is entirely my fault, and not in any way a reflection on the instructors or the material I used. If you find serious mistakes, please reach out and correct me (but please be kind and constructive with your criticisms). I would also appreciate a message if you found them helpful. Lastly, I learnt more by making these notes, rather than studying them, so I’d encourage you to make your own notes and use mine as a backup.

  1. The folder currently contains 16 Biology, 1 HSS, 4 Earth and Climate Sciences, 4 Chemistry and 2 Transdisciplinary courses; which are all the courses (with good notes) I have credited so far.
  2. Few courses have an index in the beginning, where page numbers correspond to the page number written at the corner. For a few courses, I have also scanned the summary sheets at the end, as well as quizzes/assignments.
  3. Significantly incomplete notes: Ecology 2 and Animal Physiology 2 are somewhat incomplete - Ecology 2 doesn’t have all the notes from the assigned papers, and I missed quite a few of AP2 classes and suffered for the lack of recorded lectures. General Physical Chemistry notes are also incomplete towards the end. Evolution of Landscapes notes is incomplete in the middle, which covers modules on plate tectonics and the Himalayas, which were covered by Dr Ramendra Sahoo.

The PDF files are linked to the course names in the table below. If you have any questions or comments, please feel free to contact me via email. And let me know which notes you found the most useful :blush:

Course Name Semester Instructors
Ecology and Evolution Fall 2020 Dey
Systems Biology Fall 2020 Assissi, Ghoshe
Cell Biology Spring 2021 Pucadyil, Balasubramaniam
Physiology Spring 2021 Matange, Subhedhar, Barua, Rath, Ghoshe
Genetics Spring 2021 Rikhy, Ratnaparkhi
Bioinformatics Fall 2021 Madhusudan
Neurobiology 1 Fall 2021 Subhedhar, Nadkarni, Nixon
Ecology 1 Fall 2021 Barua
Animal Physiology 1 Spring 2022 Subhedhar
Introductory Immunology Spring 2022 Rath, Bal
Animal Behaviour Spring 2022 Rajan
Mathematical and Computational Biology Spring 2022 Assisi
Ecology 2 Spring 2022 Barua
Disease and Discourse Fall 2022 Matange, Sancheti
Evolution Spring 2022 Dey
Animal Physiology 2 Fall 2022 Subhedhar
History of Political Thought in India Spring 2023 Redkar
Evolution of Life and Earth Spring 2020 Tripathi, Chattopadhyay
Introduction to Climate Science Fall 2020 Mani
Principles of Planetary Climate Spring 2021 Monteiro
Evolution of Landscapes Spring 2021 Banerjee
General Physical Chemistry Spring 2020 Hazra, Nag
Inorganic Chemistry Fall 2020 Vaidyanathan, Boomishankar
Organic Chemistry 2 Fall 2020 Chakrapani
Analytical Chemistry Spring 2021 Jayakannan
Thermodynamics Spring 2021 Musthafa, Choudhary
Data Analysis Spring 2021 Shekatkar (SPPU)

PhD Application

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Here are some useful resources that might help you with your own graduate school application -

  1. My statement of purpose for Rockefeller University (specific 3 part question), Princeton University (research statement and personal essay) and ISTA (standard 2-page SOP).
  2. Some blogs that talk in detail about the application process, from writing SOP and preparing the application to the interview and selection process -
  3. A shared Google Drive folder containing SOPs, CVs, and emails to professors collated by NYU psychology and neuroscience PhD students.
  4. Advice on how to reach out to professors you want to work with - So, you want to go to grad school? by Jacquelyn Gill.
  5. Your friends are not your competition! It really helps to have a buddy or a small group of people who are also going through the harrowing PhD application process – writing an SOP can make you feel like an imposter. So it’s good to have people who will give you feedback and keep you motivated as you go through it.

Research Project Organisation

Here are some ideas on how to organize a research project such that it’s searchable, accessible and backed up for (mostly) your future-self and your collaborators or colleagues. These are things that I have developed over the last few years and have worked well for me, but you might have different priorities or constraints. Let me know how you keep things organised!

  1. Use a reference manager to collect and manage papers. I personally prefer Zotero, especially because of the Google Chrome extension that allows you to save papers directly from the web. I also use Foxit PDF reader to highlight text and make notes directly on the PDF file. image
  2. Make sure your notes are searchable and backed up. This applies to all notes such as, literature review, meeting notes, ideas file, experiment log and so on. I used to use Google Docs for note-taking because it also makes sharing easy, but I will be moving to Github + Markdown soon. Others prefer Notion or Microsoft Word files, but it’s really important to me that my notes are on a cloud and I can access my notes from another device. The good old pen-and-paper really helps me think, and I use it to take notes during talks, but I ensure that I transfer the important points to my official notes folder.
    TIP : Name all your files in the YYYYMMDD format (with underscores instead of spaces!) so you can find them easily. This also helps avoid naming files as ‘thesis-final’ and ‘thesis-final-2.0’.
  3. Create ‘Resource’ sheets when you’re coming up with an experiment protocol or learning a new tool. For instance, during my master’s thesis, I learnt to configure (surprisingly error-prone) Raspberry Pi’s. I documented the steps and common errors along with their solutions in this note. I also documented the experimental protocol, as I was developing it, in this note. Documenting my work this way helped me to already write up the methods of my work way before I started writing the thesis.
  4. Create a summary spreadsheet of your experiments. While most experimental labs insist on a physical lab notebook to document what went down during the experiment, I also find it very useful to create a spreadsheet with all the relevant details that can be accessed easily.
  5. Document your code! This one seems trivial, but we often get lax about it. Comment and document your code for your future self. The Good Research Code Handbook by Dr. Patrick Mineault is an excellent guide on how to organise and document your code. It also has helpul advice on writing decoupled code and using unit tests to improve your code.
  6. Keep track of long-term and short-term goals. The credit for this goes to Dr Raghav Rajan at IISER Pune, since I started implementing this based on his suggestion during my semester project in his lab. I do this by creating a document where -
    • At the top, I write down the broad aim of the project, the expected results of the experiment and what it implies in terms of the bigger picture.
    • In the next section, I write the broad stages of the project and then the smaller steps, within each stage as I do the work, to keep track of where the project is heading and all the things I attempted.
    • To keep track of short-term, actionable goals - every Friday afternoon, before I log off, I make a list of all the work I did that week (including any important meetings, talks or conferences), the tasks to be done in the next week (crossing checklists is my favourite thing!), highlight any new conceptual ideas I had, and anything that was challenging that week (everything from a mental funk to frustratingly faulty equipment). This weekly update to myself keeps me on track and allows me to reflect on what I’m doing as I’m doing it.

Offering Feedback and Guidance

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Three years ago, I would spend days drafting and editing emails to professors to inquire about research opportunities. I would often run it by my friends or seniors, and their feedback on my emails, CV, SOPs and presentations significantly improved my work. Their input helped me overcome trying to get the text ‘perfect’ and boosted my confidence in my writing abilities. Vishu Guttal’s advice on how to write emails to professors is also absolutely invaluable!

If you would like an extra pair of eyes on your writing or work, please feel free to reach out to me. I’d be happy to talk about my experience and give you my feedback (perhaps with a slight delay). But keep in mind that my qualifiations are just this: a first-year PhD student, who went through PhD application process, and has some experience presenting at symposiums and conferences.

Additionally, if you’re travelling to Vienna (and Europe) for the first time, particularly if you’re a woman from a marginalised background, I would be glad to help you navigate the city in the first few days. I can offer tips and help you settle in during your initial days. Just send me an email a few days in advance.

PS. I’m starting my PhD in September 2024, but will likely only be of help in Vienna from 2025 onwards!

Miscellaneous

Metadata of compiled resources

Useful tools for scientific illustration and visualisation

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Useful tools I’ve used in my research

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If you know of any cool resources for writing, reading, research, visualisation or anything else you think might interest me - do send it along!

The comics in this page have been borrowed from PhD Comics, created by Jorge Cham. It’s a comic strip about “life (or lack thereof) in academia”.