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
• At least previously, I had some difficulties being able to preform my own microarray experiments
• However, to be honest, I think the best fit for me would be to keep doing mostly or entirely computational work (as a Bioinformatics Specialist, Bioinformatician, etc.).
• 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

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

10/7/2020 - add note about computational emphasis

Personal Thoughts on Collaboration and Long-Term Project Planning

Our opinions can change over time, and some long-term effects may not be noticeable until 5+ years of experience.

While I still don't think I have everything figured out, I am using this page to organize my thoughts on some topics that may be of use to the broader community.  I also hope that the update/change logs may also be helpful for giving credit to feedback from others during discussions.

Nevertheless, for these posts, I am going to try and focus on what I believe I understand most clearly:

• Post-Publication Review
• Staff in Shared Resources
• Long-Term Maintenance / Support
• Code / Data Sharing 

Again, it is probably a little early for me to be giving advice (since I don't have a solution worked out for myself yet), but I hope sharing my experiences can be helpful to other people as I sort out the details for figuring out a sustainable workload for myself.  Having the patience to work on agreed processes step-by-step is also important, but I believe some of this information may be important for future changes (even if they don't occur in the immediate future).

To be clear, I very much enjoy working with collaborators as a Bioinformatics Specialist in a Core Facility.  So, while some of what I am saying indicates room for future improvement, I have an overall positive impression of my work environment and the researchers that I have worked with (who are passionate about helping other people).

Plus, even though I think some of this content is important for long-term discussions, I also want to emphasize that you can be genuinely proud for putting in your best effort to help people and there is some need for short-term support (such as a temporary difficulty in getting additional funding) or at least giving people the chance to think carefully about whether a more major transition is necessary.

Update Log:

7/26/2019 - public post date
7/29/2019 - trim down introductory paragraph
7/30/2019 - add link for maintenance / support, and modify preceding sentence
8/4/2019 - minor edit after some proofreading by a family member
8/6/2019 - minor changes
4/30/2020 - add link to code / data sharing details (either required or suggested)

Personal Thoughts on Collaboration and Long-Term Project Planning: Staff in Shared Resources

While I am still having discussions to understand and precisely describe my 10+ years of genomics experience (and the influence on current projects, particularly those started Post-2016), I have some opinions that I would like to share for broader discussions:

1. If bioinformatics support comes from a shared resource, I think there may be benefits to limits on percent effort (as a fraction of split salary) and/or PIs supported by individual staff members.  A colleague kindly referred me to this paper that recommended a minimum limit of 5% effort.  My tentative opinion that there may be a benefit to having a maximum limit of 4-5 PIs (although the specifics probably vary, depending upon whether the analyst has a Master's Degree or a PhD, for example).
• For me, I feel very comfortable in saying that I need to have a maximum limit of 3 average difficulty projects per day.
• Also, if possible, I believe that gaining in-depth knowledge on a limited number of projects should help with publishing higher impact journals and/or novel methodology.
• I think this matches the minimum level of effort for NCI awards, as well as the concept of having a conflict of commitment.  I also learned about both of those at work.
2. I believe the PI / project limits for shared staff should be more strict when developing software that requires long-term support.  It is important to remember that the average (or minimum) amount of time per project will be inversely related to the total number of projects.  So, if you want to provide prompt feedback to users of your software (and fair support for all projects handled by an analyst), this needs to be taken into consideration when scheduling projects.
3. If an analyst is supporting multiple labs, I believe the best-case scenario may involve splitting time between labs that knowingly collaborate with each other.  For example, if the set of projects among all labs is known, that may help scheduling submission (and expected revision) for papers that are expected to be published in the highest impact journals.  Regardless of whether this is done, the ability to support any given project is dependent upon concurrent support of other projects, and I think that is at least something that needs to be kept in mind.
4. I think there should be transition periods when making changes in staff support.  While I'm not 100% certain about the details, I think a yearly or quarterly review may be a good idea.  I don't believe it is a good idea to make support decisions on a daily or weekly basis, and it often takes me 1-2 months to feel comfortable with a project that has been was previously worked on my somebody else.
5. At least for me, it helps to have somewhat frequent discussions / analysis to help remember the details for a project.  For example, I would probably recommend having at least monthly discussions (and I think weekly or daily discussions / analysis is probably preferable).
6. Likewise, I can discover and fix errors when spending a substantial amount of time for critical assessment of results.  For example, my recommendation would be to expect to have 10 "rounds" of analysis (hopefully, some of which includes creative / custom / novel analysis).
• This isn't perfect, but I know I have found (and corrected) some errors this way.  This is kind of similar to being able to make new discoveries (or correct additional errors) when you re-read a paper.
7. It is my opinion that specialized protocols should be an area of expertise for individual labs (which may or may not be offered externally), but this should not be a responsibility / service of the core.

That said, I am expecting the "Update Log" to reflect at least a few additional changes (as I have more discussions - primarily internal at first, but I think some broader feedback is also valuable).

While I am primarily focusing on the project management part of shared staff in the points above, the concept of an optimum workload can be important in various situations.  For example, if your optimum workload is 5 projects and you are trying to take on 10+ projects, you will either do lower quality work or not have an even distribution of time on projects.  However, that does indicate a possible solution: if somebody is having difficulties with supporting a certain number of projects / PIs, they may actually be able to be capable of producing excellent quality work if they focus on fewer projects more in-depth.

Update Log:

7/26/2019 - public post date
9/14/2019 - add note on discussion intervals
9/16/2019 - remove nearly duplicated sentence
9/23/2019 - mention being able to catch errors as I perform additional analysis for a particular project
9/28/2019 - add point / opinion #7
4/16/2020 - add link about effort limits and conflict of commitment
4/17/2020 - minor change