PhD Insights and Reflections

Introduction

Why PhD

At the time

Deep dive into a topic of interest. eventually interested in translation but wanted to train fully to do basic research. Expertise, approch, ways of thinking. chance to go abroad widen my exposure.

In retrospect

Beyond the techincal aspects of the project. philosophy of science. approach to reserach. my reflection - rethinking how we choose our questions. hot take- doesnt really make you industry / job market ready. mostly projects are individual driven, no tight timelines, few stakeholders and mostly with the same background and motivations. but it does provide a platform from which to make yourself so if you are lucky with the lab and location.

Why Switzerland {.tabset}

At the time

lab I wanted to work in happened to be there

In retrospect

One of the best phd salaries. Active innovation ecosystem. great work life balance. good quality of life. beautiful country. but cultural and language barriers to surmount for success. particulary pivoting out of academia is challenging especially for “third country nationals” (non-eu).

How did I get there {.tabset}

At the time

contacted PI cold but 3 follow up emails. Was happy to support, great zoom chat. FBM fellowship. What helped: was working on microbiome and new dna sequencing tech that the lab was also expanding metagenomics and bioinformatics using NGS. Demonstrated interested in biotinformatics had not done a lot of it but familiar with R (ecology course work for a start), bash (enthusiatic friends who got me into linux), getting familiar with snakemake (curiosity and challneged myself to use it for masters thesis). This combined with wet lab work experience in previous project.

In retrospect

right place right time. demonstrated interest in forward looking area not just what the lab was working on at the time. Good profile for international FBM fellowship and interview went well. funding environment good. More challengning now even in switzerland.

Celebrating the defense

inspiration for a multi-cultural celebrations? - Apero with bread and cheese followed by south indian snacks (sundal, idly, podis), german mini sausages and cakes for dessert.

Advice: Read passicvely go back to mosr inspiring ones collect theses you respect and get inspired very detailed breakdown to-do list informal close-knit peer group - share said list living document review for busy PIs culmination of past 2 years of reading not just these 2 months of writing remember that adding new directions is a disservice to the almost completed sections if artistic make drawing for fun even if it doesnt really go into the thesis zoom co-working with trusted peer or friend

Example plans Updates on the plan (very course timeline plan): This week (21-25th Apr): Complete Ch3 draft Write up discussion Other sections cleaned up Share draft for feedback Get working on General Introduction by section after Next week (28th Apr - 2nd May): Write paragraphs of Ch1/General intro as time permits Trip including a few activity-free days (2nd May) - Lab celebration Week (5 - 9th May): Write up the Ch1/ General Introduction Write Ch3/ Summary and revisits Ch2/ Summary Draft Abstracts and share for feedback Week (12 - 16th May): Complete Ch4/ General discussion Incorporate feedback on Ch1/General Introduction Incorporate feedback on Abstracts Write Acknowledgements Incorporate feedback on Ch1/General Discussion Week (19 - 22nd May): Prepare overall draft (with CV etc. other sections needed) Polish and proofread Additional embellishments (figures, cover page) Combine manuscript PDFs and supplements. material Thursday (22nd May) - Send the thesis draft to the committee and doctoral school

and I mean really detailed:

Compile figures and tables for priority effects chapter Polish code and clearly separate out the code that is being used to make figures Fig 1 - experimental design - mostly done Fig 2 - pcoa plots - polish them some more Fig 3 - show colonization in box plots (first and second) for each strain Replot without shape for each community combo (include more details plot(s) in supplementary compile panels in a compact way for the figure Fig 4 - boxplots of priority effects of each strain - show median or bootstapped - leaning towards median - include bootstrap in the supp. Table 1 - GLMM results for abs_counts ~ arrival_order + random effect community combo Fig 5. Dropout treatments Streamline boxplots Show stats Fig. 6 about the interesting strains’ gene content - postponed/skipped for now Compile supplementary figures for priority effects in the chapter (there are severaaall!) - start outlining text to make more insights from pilot exp. - not including pilot samples in further plots or supps more details on the community compositions sequencing success + qpcr + detection limit per sample.. show that MD bees are “clean”, extraction blanks schematic of asv detection approach exact abs counts of all strains in all samples … Supplementary tables Genome info (species, ANI etc.) Community compositions counts and other info tables for all samples samples metadata / experimental treatment information Write an outline of the results (If time permits) work on the methods section Additional polishing of reviewer comments on Apis species manuscript