Need a Bioinformatics Job?

 

TL;DR. Job hunting advice from a guy with a good track record of landing bioinformatics jobs.

I woke up this morning with the urge to give some bioinformatics career advice. The bioinformatics job market right now is tight. It is difficult to land a good job, particularly for those who are ill-prepared.

Assumptions. You know what bioinformatics is and you are interested in working in the field.

Old Bioinformatician. I am one of the oldest career bioinformatic scientists out there. Not the oldest by any means, but I’ve been in the field of bioinformatics since around 1999 and did a fair amount of wet-lab before that.

I probably shouldn’t, but I read comments on Reddit r/bioinformatics and r/bioinformaticscareers all the time. And those two subreddits are full of people who don’t understand the field. You will see comments like “I applied to x hundred jobs and didn’t get a single interview”.

Buddy, you didn’t apply to a hundred jobs, you spammed a hundred employers. I have a master’s student who was looking for a job. We would look at each job description. I’d help him understand what they were looking for and what the work would be like. He would then craft a cover letter and resume for that position. He applied for about a half-dozen jobs. Got two interviews and an offer. (Of course he was well qualified and a great student.)

To apply for a job, you need to make it clear to the hiring manager why you are the right person for the role. If you just spam them with some premade documents and force them to try and infer your qualifications, they will ignore you in favor of the person who put the time into applying for the only role the hiring manager is currently looking to fill.

There’s an App for That. But that’s not what motivated this post. There is a population of bioinformaticians who approach bioinformatics incorrectly. I’ve been struggling for a long time for a way to articulate the problem, and recently I was talking with my wife about a student I had a consult with, and she came up with the phrase that summarizes the problem, “There is an app for that.”

In translational medicine we very frequently come across omic studies with complex experimental designs. We might have multiple samples from a patient, before and after treatment, affected and unaffected tissue, and blood. And they are almost always unbalanced designs. And there are frequently repeated  measures and time courses and all sorts of good stuff.

I work in a Medical College so the task of analyzing the data will go to some master’s student who has no specialized bioinformatics training. They will learn a little programming and some statistics, and they will lean into their assigned problem. These students are not the problem. My job is to help them learn how to correctly analyze the data. But it was one of these students that helped me articulate my concern.

This student had a complex experimental design with hundreds of samples all run through the appropriate discovery omic, for conversation, let’s say it was bulk RNASeq. They need to perform a differential expression analysis to find those molecular entities that are changing between before and after treatment etc.

They come in, we do a little prep work to get them ready, and then I routed them to our drop-in statistical coaching service. In this student’s case, they got a little over an hour with one of our PhD biostatisticians. I joined in for a bit of the conversation. They were given some instructions on what to do for next week (Drop-in stats is every Tuesday at Two) and they went away. They were to articulate a list of all the specific questions they wanted to ask the data and some other stuff. And then come back and we would work on the model statements for their analysis.

Three days later, they swing by my office. “Hey Rich, did I do this right?”

“What did you do?”

“I ran it through a specialized R library I found. It’s written for this type of data. I ran it with the default parameters. It should be right, right?”

If you do the math wrong, you get the wrong answer.

The probability that a bioinformatic tool will default to the correct parameters for your obscure experimental design are asymptotically approaching nil. I sent him off to see if he could find what model statements the tool has auto-magically generated before it sent them into LME for him – and we hope it was LME, it might have passed the differential expression analysis to a different library. Who knows.

The student assumed that if there was an “app” for the job, it would just work. And when it spit out p values, they must be the correct p values.

But this is my job, not a problem, they are a cleaver student and will quickly see where the biostatistician and I are guiding them. That’s not the problem.

The Real Problem. The problem is that a lot of bioinformaticians are learning to hit data with “apps”. Like the student, they are trusting that the tool will do all the correct steps without the operator needing to know what those steps are.

“If it is bulk RNASeq data, I run it through DESeq2, I get the differential expression results and I send it on to the next step in the workflow.”

But bioinformatics is mathematical inference—each computational step needs to be undertaken for a reason—and the researcher needs to understand both the reason for the step and how to perform it.

Nowadays, at least in translational medicine, almost all experiments are performed by a large team. Not every researcher on the team needs to understand every step in the computation, but they need to be able to trust that their bioinformatician does.

And there are an endless number of tools being written which do some neat, and worthwhile computation, and then the tool’s authors just tack onto it a few other steps so the tool can complete a full workflow. Some people treat these as “Apps”. They assume that the tool will do “its job” and that the numbers that come out are correct.

Unfortunately, you have to understand 1) what the tools is actually doing, 2) what computation you need in order to make your inference, and 3) what the question actually is that you are trying to make an inference about. So, in order, you need to understand the computation, statistics, and biology of the problem.

Career Advice. I see many students who are taking programs which teach you that this tool reads in this kind of data and spits out those numbers. “There’s an App for that.”  This is fine for two situations. First, if the experimental design of your data exactly matches that of the tool, it should work. Second, if there is a researcher above you who knows what they are doing and gives you the exact right instructions. In either of these cases, just knowing how to manipulate data to form the correct input format and graphing the output will be sufficient.

But, in my experience, most people who are looking to hire a bioinformatician aren’t looking for either of those (usually, those types of jobs do occasionally come up). Instead, they typically are researchers who understand the bench part of the job, and they need someone who can understand the computation and inference parts.

So, my career advice is, 1) show that you understand their needs. Don’t make them guess or try and read between the lines. Write your cover letter to exactly match the tasks in the job description. 2) Be brutally honest with your own limitations. Most hiring managers want to know what you can and cannot do. If you claim you can do everything, you end up looking like a duffus that no one would want to hire.  For example, I can’t write complex model statements in R. I’m a SAS guy. So, if we need a complex model in R with nested effects and random this and fixed that, I defer to the biostatisticians. But I can at least understand the design. 3) Remember that you are applying for a role in a team. Show that you can work well with others. That you listen to what people are saying and that you understand your own strengths and weaknesses. And the best way to do this is to listen to what they put in the job description.

Anyone can write some R code or Google what tool to use. Showing that you will be an asset to the project will increase the probability of getting the interview. And interviews lead to offers.

Good luck And, as always I thank you for reading my posts and remind you that I welcome comments or questions below.

A Little TTRPG relief from this Crazy World

 TL;DR. I drew some maps that I think are neat, and I’ve added some text describing a low-key fantasy setting that could be used as a starting point for something like an OSR Dragonbane or Mythras game or could act as a center point for either a low-stakes politics or cozy fantasy campaign.

 

I’ve been kind of quiet for a while, so I wanted to show you one of the things I’ve been working on. It is the type of fantasy setting my friends and I would have played in in the late 1970s. Would would have used Runequest rules and would have had much worse maps. Enjoy.

Gevensthorp is a small, fantasy settlement located on the shore below some highlands at the end of a long, narrow bay. It is (at first glance) a peaceful place, but it is secretly brimming with low-key political, cozy, or even OSR fantasy adventure—depending on how you want to play it.

1. The Thorp

Along a road that connects the bustling village of Redworthy and the villages, castle, and mines on the northern headlands, there is a small settlement composed of a few stone houses built from the obvious remains of an old fortification.

A. The Blemished Boar. Run by Geven the Younger (who is now in his 40s) and his wife and children, this is a small inn/tavern/roadhouse that is always busier than it should be.

B. The Houses. Across the road, there is a row of stone houses. The northernmost house is the home and shop of Geven the Elder, an accomplished blacksmith.

 All the other homes are occupied by his children and their families and friends.

C. Farms. Geven’s oldest daughter and her family manage a small farm which doesn’t provide enough to feed the whole community, but it does well for its size.

D. The Old Bridge. At the south end of the settlement is an ancient stone bridge built in the style of the Old Empire with a small two-story toll booth and home built on one side. There hasn’t been a toll in generations, but the home is usually occupied.

Secrets.

1. The oldest, and best kept secret is that Geven the Elder was once the armorer to the King and his wife was the Captain of the Queen’s Guard. They eloped and ran off together and settled in this out of the way corner where they lived a peaceful life and raised their family. Their youngest daughter, Crystal, still lives at home and has no idea of her parents’ past.

Occasionally, strangers still come to call and once a year or so Geven the Elder will craft a sword for one of them. The family lives a rustic life, but they never seem to want for money.

2. Just south of the village there are trails which head up into the highlands. They go to some old ruins, but they also connect across the highlands to the Eastmark. Although there is currently no open hostilities with the Eastmark, they are not part of the kingdom and trade with them is regulated. None the less, every week or so, a small pack train of mules comes from the mines laden with ores. These travelers stay the night at the Blemished Boar, and in the morning head into the highlands. When they return, they are usually loaded with crates and barrels.

2. The Tower of Laricus the Wise. A crumbling old castle, with the great hall and main tower burnt, the thin, outer walls in ruins, is just of the highland trail. This is the home of two mysterious, old wizards and their apprentices.

3. Chestnut Springs. A magical hot spring, and ancient and sacred pool, and a small grove of spirit-infested oaks form an unusual temple at the headwaters of the stream.

Three possible sites of adventure are just north of the settlement.

4. The Long Barrow. Long before the arrival of the Old Empire, which itself was long ago, someone built a massive stone structure and covered it with earth. Why? And what is inside? Maybe a small dungeon. Maybe a necromancer’s lair.

5. The Sea Cave. A deep, sea cave is cut right at the waterline. Is it the home of a sea hag, or some other creature? Have pirates built a secret lair to hold their treasure?

6. The Abandoned Toll-Bridge. Although the bridge is crossed weekly by pack trains, and once or twice a day by legitimate foot traffic, it is possible that the abandoned toll-house has attracted visitors. Maybe brigands looking to lay low or maybe a goblin or orc looking for trouble.

 1A. The Blemished Boar.

To the trained eye, the barn of the Blemished Boar was once a royal long house. But those style of structures fell out of use at least a century ago. Now it is just a well-made stone barn. Likewise, the unusually strong outer wall is clearly the remnant of an even older fortification. Most evenings the Boar is crowded with locals and a few guests. It is rare that there are more than half a dozen people staying the night, but it is not uncommon for folks to travel the few miles from Redworthy just to enjoy a visiting entertainer or a good batch of local ale.

 2. Tower of Laricus the Wise.

Laricus the Wise and the School of Esoteric Magic. A short walk from Genensthorp is the burnt out remains of a castle. The structure was a lightly fortified house, perhaps as recently as a century ago, but now the partially destroyed building is the home of several eccentric spell casters.

Laricus the Wise is an ancient man and a master of arcane magic. He may have an identical twin brother Daricus, or he might have a personality disorder. Reports differ. Either way, they never physically leave their tower. Instead, they spend their time exploring the mysteries of the Ethereal plane and those existences that can be found beyond it.

They maintain a small compliment of students who are mostly self-teaching themselves magic, but they do receive an hour or two of instruction from the master’s every week or so. In exchange, they have access to some of the items the masters collected before retreating into their tower. Generally, the students like the arrangement and are loyal to their teacher (or teachers).

A. Wizards Tower. When the masters hold class, they do so on the lower floor of the tower. The upper two floors are windowless and unseen by anyone other than the wizards. The lower floor has a chained library, a permanent magic circle and other items useful for learning magic.

B. Guest Tower. The wizard’s advice is often sought by outsiders, and the base of a small tower survives and has been converted to a guest room.

C. Tall-Tower Cellar. The main structure was once a tall tower next to the great hall. Both structures burnt a long time ago, leaving the hollow, stone shell which extends several floors upward and the cellar or ground level which was made completely of stone. The base of the tall tower has the only surviving entrance and the heavily vaulted room has been converted to a meeting room. Since the Masters will only see people (typically) one morning a week, when visitors arrive, they are usually first met by the students. And this is the space where they meet them.

D. The Kitchen. Once the kitchen for the entire castle, this space is now the common area for the students. They prepare their own meals, manage their own supplies, and generally use this space as their common room.

E. The Museum. The wizards have a bunch of stuff that is stored in this central space. Nothing of epic-power, but lots of small items that are useful in understanding the nature of both the physical and magical worlds. The students call it the museum and are often in here searching for clues to understand this or that rune or arcane formula.

F. Student Space. Once specialized storage areas for the castle, these small, stone-vaulted chambers are now the sleeping and practicing spaces for the students. Typically there are three to eight people studying magic here and the level of harmony withing the student population often reflects how crowded these spaces are.

G. Kitchen Cellar. Under the kitchen there is a dark and cool cellar that was formerly used to store food for the castle. The first section is still used for this purpose, but the students have taken over the back sections to serve as additional practice space.

 

3. Chestnut Springs

Nestled on the slopes up to the highlands, in a small and sheltered valley, there is a grove of ancient oak trees partially surrounding a mystical hot spring and a sacred chestnut tree. The site was once popular for the healing properties of its spring water, but the scattered ruins nearby attest to the decline in visitors over the last few decades. There are typically one or two clerics who tend to this holy place and depending on their nature, they may also be students of the wizards just down the trail.

A. The Long House. Built of salvaged stone, but in a style usually reserved for the people of the north, the long house accommodates both the clerics and any guests.  It can easily accept seven guests but is seldom called upon to do so anymore.

B. The Chestnut Pool. An ancient chestnut tree sits on a small (likely artificial) island in the center of a pool feed by two aggressive hot springs and partially enclosed by the old oaks. The site is understood to connect directly to the divine, but only the most devout will enter the upper pool due to its heat.

C. The Pool. During the centuries that the Old Empire ruled, a large wading pool was built. Here, the water has cooled enough that it can be enjoyed by those seeking healing or spiritual growth.

D. Pixie Pool. Small, natural pools have formed from the out-flow of the main pool. Some people believe that this site attracts pixies who live in the oaks, but others disagree. Either way, they are called the Pixie Pools.

The remaining sites are left undefined so that GMs can customize the location for their own games.

As always, if you have read this far, I thank you for your time and welcome any comments or questions below.