Thursday, November 14, 2019

What do I need to change as an individual?

I can tell that I need to work on fewer-projects in more depth.

I am not sure if additional training is necessary to accomplish this, but that is the focus of my post on "What are the expectations for Individuals with an MS in Bioinformatics versus a PhD in Genomics?"?

Technique-Wise, these are the sort of things that I think I could be comfortable with:


  • I am very comfortable coding in R / Python / Perl
  • If I needed to get back into the lab, I could previously do a PCR and maintain a cell line
  • I think I likely need to reduce the number of new patient samples that I encounter, but I am comfortable working with my own genomics data and I think I have had useful contributions using re-analysis of data deposited by other labs.
    • For example, I thought this was a relatively successful story of my feedback on a pre-print being helpful
    • I also have notes on my human genomics results here
    • I also have on-going analysis of public cell line perturbations to demonstrate method limits for RNA-Seq analysis
  • At least previously, I had some difficulties being able to preform my own microarray experiments


Research-Wise, there are topics that I am interested in and/or have some prior experience with:


  • Investigate whether a relatively simple strategy is more robust than a more complicated strategy (for example, try to identify problems with over-fitting)
  • Probably a good idea to either limit the number of samples I work on at a given time and/or make sure that I have enough time for several rounds of analysis / discussion of the same dataset (which is always good for critical assessment of results)
  • Perhaps place more focus on non-human genomics (and I started out doing evolutionary genomics research)?
    • I have some previous virology experience, so perhaps I could study the genetics / genomics of viruses that currently infect other animals (but have not yet evolved the ability to infect people)?  This could even be part of DNA-Seq or RNA-Seq for the host.
    • While I haven't done any such research from a professional standpoint, I have been comparing genomics results for my cat Bastu, and I hope to have a blog post summarizing that soon.
  • If I can get agreement about some things, perhaps there is some value in shared support guidelines?
    • I also truly like the idea of supporting labs with less popular research topics and/or smaller budgets (which may have a relatively greater need for shared support)
    • Essentially, I am emphasizing training (indirect analysis support) and limits on projects for shared staff
    • However, I don't particularly like telling other people what to do (the degree discussion is really more about having the right amount of autonomy and peer respect to perform my own analysis), even though I realize that we sometimes have obligations to society to do things that we may not find enjoyable.
    • So, I think finding a solution for myself what is currently most important, but I think I have some experiences that may be useful to others.
    • In general, if I were to assist with training support, I think I may be able to help with common public datasets, but I think there may need to be a rule that I couldn't help with providing analysis for a new dataset (unless a greater commitment to the project is made, where the limits on shared support would then be important)
    • While helping me stay up-to-date and refreshed on details, perhaps providing local guidance (face-to-face) for a subset of content from selected on-line courses (like Coursera) may be an appropriate way for me to help, but it would be crucial that I not complete exercises for any students (which would violate the honor code, requiring students to complete their own work and demonstrate independent competence).  For example, if I did this before they started the course, perhaps I could then recommend where to learn more and get certification (as well as setting realistic expectations on the likelihood of passing the course).
  • I would need a lot of practice, but outreach / optional education for the general public (such as a book club discussion that I led) can be rewarding 
  • While I am less certain about my role in a professional standpoint, you can see my "speculative opinion" posts about some things that I think could be interesting


Personality-Wise, these are what I believe are my strengths and weaknesses:


  • I have to be fairly independent for my current job, but I do provide a supportive role (where biological / clinical idea usually comes from PI)
  • While the difference between 1 day and 2 weeks turnaround time would be an order of magnitude (for each iteration of analysis/discussion), I have received the good suggestion that I should wait at least an extra day before returning each round of results (to see if I can catch more errors by reviewing the results again the next day).
  • I like the idea of helping provide a "public good," so I think I would prefer to continue working at non-profits
  • Continue becoming better at more mindful when I have a prior assumption (which may or may not be true) and I may not sufficiently understand other perspectives.
    • However, I appreciate those who value the need to take time to be objective and fair
  • While I believe it is important to continue to make future progress, I have some concerns about responsibilities what require excellent communication (and would frequently involve relatively short interactions with individuals where I may not have the chance to correct myself)
    • For example, part of the reason I work on the computer is that I bugs will stay corrected in the code (once I find them).
    • In contrast, if you knew that there was an experimental protocol that required X steps and I was highly like to mess up at least 1/X steps, then that is sufficient for me to not be able to get a protocol to work (for example, I think this is why I had previous difficulty with performing my own microarray experiment).
  • I think I may need to better recognize what I can fix (for myself), versus a concern about the actions of others (which may be solvable if properly communicated, or may be harder to resolve without common agreement)
    • For example, there may be some room for improvement in terms of communicating myself in sensitive situations (such as disagreeing with a policy and/or a superior).  However, this is something that I am actively working on.
  • Most of my family lives on the east coast of the United States (and I currently live in the west coast, in California).  As we get older, this may be something worth taking into consideration.



Change Log:

11/14/2019 - public post
11/15/2019 - public post
11/21/2019 - fix typos + add waiting a little longer to return results
1/7/2020 - add link for on-line course notes
4/30/2020 - update cat link for blog post versus GitHub

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My Biomedical Informatics Blog by Charles Warden is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States License.