Bioinformatician growth
A bioinformatician on my team is always looking to grow and improve their skills. These checklists help identify the skills to develop and the knowledge to acquire.
The checklists are the minimum required to move to the next level. The full set of requirements is discussed and agreed with the manager. You need to complete every checklist item to advance, but completing them all does not guarantee advancement: the manager may also set individual requirements.
My team works in oncology and mainly deals with NGS data, so some items are specific to those areas. Some of the linked learning resources are in Russian.
Trainee
Knows the basics of molecular biology, statistics, and NGS analysis. Understands the null hypothesis, p-values, Fisher’s exact test, the chi-squared test, the t-test, the Mann–Whitney U test, and multiple testing correction.
Can run a Jupyter notebook and use Python to read a data frame, filter its columns, and draw a histogram and a scatter plot.
Learns the principle that working on something is not the same as getting it done. Shows relentless drive. Will revise test assignments and work tasks ten times if needed, persists from the very first tasks, and is not afraid of unfamiliar topics.
Takes responsibility. The particular task matters less than the ability to take ownership and deliver a result. Volunteers to keep time at a team meeting, find the person responsible for the office and get a chair repaired, work out how to download a dataset, or set up an agent and write instructions for colleagues.
Learns to organize their work. Until they gain experience, works on simple, routine tasks under close supervision from senior colleagues. Keeps track of their tasks and takes meeting notes without being reminded.
Studied
- The basics of molecular biology
- The basics of statistics, for example the two-part Stepik course: part one and part two
- The basics of Python or R
- The basics of NGS, for example on Stepik
- Clear written communication: headings, captions, links, and quotations in messengers and email
- Google Docs: formatting, styles, and access settings
- Google Slides
Read
Delivered
- Completed a project under the supervision of senior colleagues and presented the results
Bioinformatician
An independent operator. Handles routine tasks independently and complex ones with a manager’s support, without constant supervision. Finds or requests the information they need, tracks deadlines, and raises concerns in time.
Has at least one project of their own: a client project, an internal R&D project, a Confluence space, a blog, a channel, or a product.
Learns to be flexible: resolves tensions between deadlines and quality through ingenuity and flexible scope, rather than by sacrificing deadlines, quality, or personal time.
Learns to verify rather than trust. Can establish and explain that their own analysis, or work by a colleague, another department, or an agent, is based on real data and appropriate methods and does not overlook the obvious.
Cohort analysis is a core skill. Can obtain a cohort and its annotations, assess data quality, analyze genetic events, and put the results into a presentation.
Is well read and well prepared. There is no such thing as a bioinformatician who has not read Hallmarks of Cancer or cannot write a skill for Claude.
Is not afraid of unfamiliar work. Will run an agent, write code and submit a pull request, start a Docker container, inspect a BAM file in a genome browser, run differential expression analysis, or put together a presentation.
Learns to negotiate: understands the client’s problem and their own capacity, agrees on deadlines, and resolves conflicts.
Read
- Building effective agents by Anthropic
- 30 selected papers — make your own copy, mark what you have read, and use it for notes
- Claus O. Wilke. Fundamentals of Data Visualization
Studied
- Working with an AI agent on a real task: defining the task, checking the result, and finding an error
- How bioinformatics tools work and where their limits lie: BWA, Strelka, Sequenza, kallisto, STAR, and STAR-Fusion
- Sequencing quality metrics
Delivered
- Contributed to two projects led by senior colleagues
- Independently completed a research or cohort analysis project from start to finish
- Built something together with developers, taking ownership of the work
- Gave a lecture on an educational course
Collected
- 20 observations
Lead bioinformatician
Leads the team of independent operators. Represents bioinformatics to the client, from the initial request to the final result. Handles all aspects of the client relationship and takes responsibility for them.
Knows the deadlines, writes client proposals, plans iterations, and manages the project. Solves problems by designing and building a real product. Takes responsibility for its usefulness, delivery date, and quality. Answers for every chart and comma in a paper or product. Finds flexible solutions.
Chooses and supervises the people doing the work within the department and delegates tasks. Has projects of their own, a blog or channel, and maintains a section in Confluence.
Read
- Genrikh Altshuller. Find an Idea
Managed
- Independently explained a product feature to another department — developers, biologists, or clinicians — and handed it over for implementation
- Reviewed work by a specialist in another department, wrote feedback, checked the revisions, and accepted the result. In other words, made sure the work was done properly
- Independently sorted out a messy situation with another department: understood the conflict, motivated people, and resolved the organizational problem
Delivered
- Attended five meetings with new clients and asked questions
- Wrote five task briefs and got them approved by the clients
- Delivered five practical tasks under their personal responsibility: presented an analysis to a physician, submitted work to a conference, or released a component update
- Solved a problem through other people’s work
Developed
- Helped a trainee become a bioinformatician. Preferably two, or even three
Shared knowledge
- Gave a public lecture
Standardized
- Improved three things in the bioinformatics department’s work and agreed new procedures, standards, or principles
- Got five templates for replies, mailings, or pages approved
Collected
- 100 observations
Director
The defining quality is effectiveness: always knows what result is needed and how to achieve it. A director has many tasks, projects, employees, clients, and other concerns, so allocates time to influence everything that matters to the result.
An entrepreneur and strategist. Rather than solving a task as a team lead does, sets tasks in a sequence that produces the greatest effect with the least waste.
A standard setter. Improves procedures, processes, and tools. Each improvement benefits many projects.
A magician. Helps managers and teams with simple, effective advice that makes them say, “Wait, we could do that?” Does not keep track of deadlines unless the lead bioinformatician brings them up. Is the final quality check, but not the main one: that responsibility belongs to the lead bioinformatician. Does not put up with crap and keeps pushing back against deadlines — and, in effect, against the lead bioinformatician.