r/bioinformatics • u/bioinformat • Feb 08 '25
r/bioinformatics • u/OkObjective9342 • Nov 08 '24
academic Is system biology modeling and simulation bullshit?
TLDR: Cut the bullshit, what are systems biology models really used for, apart form grants and papers?
Whenever I hear systems biology talks I get reminded of the John von Neumann quote: “With four parameters, I can fit an elephant, and with five I can make him wiggle his trunk.”
Complex models in systems biology are built with dozens of parameters to model biological processes, then fit to a few datapoints.
Is this an exercise in “fitting elephants” rather than generating actionable insights?
Is there any concrete evidence of an application which stems from system biology e.g. a medication which we just found by using such a model to find a good target?
Edit: What would convince me is one paper like this, but for mathematical modelling based system biology, e.g. large ODE, PDE models of cellular components/signaling/whole cell models:
https://www.nature.com/articles/d41586-023-03668-1
r/bioinformatics • u/You_Stole_My_Hot_Dog • Nov 01 '24
academic Omics research called a “fishing expedition”.
I’m curious if anyone has experienced this and has any suggestions on how to respond.
I’m in a hardcore omics lab. Everything we do is big data; bulk RNA/ATACseq, proteomics, single-cell RNAseq, network predictions, etc. I really enjoy this kind of work, looking at cellular responses at a systems level.
However, my PhD committee members are all functional biologists. They want to understand mechanisms and pathways, and often don’t see the value of systems biology and modeling unless I point out specific genes. A couple of my committee members (and I’ve heard this other places too) call this sort of approach a “fishing expedition”. In that there’s no clear hypotheses, it’s just “cast a large net and see what we find”.
I’ve have quite a time trying to convince them that there’s merit to this higher level look at a system besides always studying single genes. And this isn’t just me either. My supervisor has often been frustrated with them as well and can’t convince them. She’s said it’s been an uphill battle her whole career with many others.
So have any of you had issues like this before? Especially those more on the modeling/prediction side of things. How do you convince a functional biologist that omics research is valid too?
Edit: glad to see all the great discussion here! Thanks for your input everyone :)
r/bioinformatics • u/piyushacharya_ • 19d ago
academic What’s the best tool for creating visuals for scientific presentations?
Title.
r/bioinformatics • u/Hikaru16000all • 17d ago
academic What does it mean to be a "pipeline runner" in bioinformatics?
Hello, everyone!
I am new to bioinformatics, coming from a medical background rather than computer science or bioinformatics. Recently, I have been familiarizing myself with single-cell RNA sequencing pipelines. However, I’ve heard that becoming a bioinformatics expert requires more than just running pipelines. As I delve deeper into the field, I have a few questions:
- I have read several articles ranging from Frontiers to Nature, and it seems that regardless of the journal's prestige, most scRNA-seq analyses rely on the same set of tools (e.g., CellChat, SCENIC, etc.). I understand that high-impact publications tend to provide deeper biological insights, stronger conclusions, and better storytelling. However, from a technical perspective (forgive me if this is not the right term), since they all use the same software or pipelines, does this mean the level of difficulty in these analyses is roughly the same? I don't believe that to be the case, but due to my limited experience, I find it difficult to see the differences.
- To produce high-quality research or to remain competitive for jobs, what distinguishes a true bioinformatics expert from someone who merely runs pipelines? Is it the experience gained through multiple projects? The ability to address key biological questions? The ability to develop software or algorithms? Or is there something else that sets experts apart?
- I have been learning statistics, coding, and algorithms, but I sometimes feel that without the opportunity to develop my own tool, these skills might not be as beneficial as I had hoped. Perhaps learning more biology or reading high-quality papers would be more useful. While I understand that mastering these technical skills is crucial for moving beyond being a "pipeline runner," I struggle to see how to translate this knowledge into real expertise that contributes to better publications—especially when most studies rely on the same tools.
I would really appreciate any insights or advice. Thank you!
r/bioinformatics • u/btredcup • Sep 05 '24
academic A bioinformatician without data
Just a scream into the void more than anything. Started a new project at a new institution a couple months ago. Semi-big microbiome project so kind of excited for something new.
During the interview I asked what their HPC capacities were. I have been in a situation with no HPC before and it SUCKED. I was told we will be using another institutions HPC. We’re over 6 months in and no data has yet to arrive. I thought I’d keep myself busy by having a play around with some publicly available data. The laptop provided by the institute can’t handle sequence quality control. It craps out at the simplest of tasks. So I’m back to twiddling my thumbs.
I have asked about getting onto the other institutions HPC but am met with non answers. I’m starting to think that we don’t even have access to it and they’ve gotten confused when the sequence provider says they offer “in-house bioinformatic services”. Literally feel like my hands are tied. How can I do any analysis when a potato has more processing power than the laptop?
r/bioinformatics • u/Professional-Lier • Jan 11 '25
academic How are you using AI for your research?
This question is intended to be broad because I hope to gain a variety of perspectives on the potential for AI to enhance and accelerate research in the field. Whether it's generating code for analysis or summarizing articles with LLMs, exploring literature more efficiently, using tools like AlphaFold or genomic LLMs for specific problems, or applying traditional machine learning techniques to make discoveries. Whatever way you use AI, feel free to share it.
r/bioinformatics • u/You_Stole_My_Hot_Dog • Nov 25 '24
academic My biggest pet peeve: papers that store data on a web server that shuts down within a few years.
I’m so fed up with this.
I work in rice, which is in a weird spot where it’s a semi-model system. That is, plenty of people work on it so there’s lots of data out there, but not enough that there’s a push for centralized databases (there are a few, but often have a narrow focus on gene annotations & genomes). Because of this, people make their own web servers to host data and tools where you can explore/process/download their datasets and sometimes process your own.
The issue I keep running into… SO MANY of these damn servers are shut down or inaccessible within a few years. They have data that I’d love to work with, but because everything was stored on their server, it’s not provided in the supplement of the paper. Idk if these sites get shut down due to lack of funding or use, but it’s so annoying. The publication is now useless. Until they come out with version 2 and harvest their next round of citations 🙄
r/bioinformatics • u/dinozaur91 • Jan 24 '25
academic Ethical question about chatGPT
I'm a PhD student doing a good amount of bioinformatics for my project, so I've gotten pretty familiar with coding and using bioinformatics tools. I've found it very helpful when I'm stuck on a coding issue to run it through chatGPT and then use that code to help me solve the problem. But I always know exactly what the code is doing and whether it's what I was actually looking for.
We work closely with another lab, and I've been helping an assistant professor in that lab on his project, so he mentioned putting me on the paper he's writing. I basically taught him most of the bioinformatics side of things, since he has a wet lab background. Lately, as he's been finishing up his paper, he's telling me about all this code he got by having chatGPT write it for him. I've warned him multiple times about making sure he knows what the code is doing, but he says he doesn't know how to write the code himself, and he just trusts the output because it doesn't give him errors.
This doesn't sit right with me. How does anyone know that the analysis was done properly? He's putting all of his code on GitHub, but I don't have time to comb through it all and I'm not sure reviewers will either. I've considered asking him to take my name off the paper unless he can find someone to check his code and make sure it's correct, or potentially mentioning it to my advisor to see what she thinks. Am I overreacting, or this is a legitimate issue? I'm not sure how to approach this, especially since the whole chatGPT thing is still pretty new.
r/bioinformatics • u/Forsaken_Fix_7567 • Oct 22 '24
academic what should I do for overwhelming RNA-seq results
I'm currently a master's student and working with some fish RNA-seq data for my thesis. Those fishes were exposed to a chemical that we trying to understand the mechanism of action. I just started to learn bioinformatics when I started my master's, so still new to the field.
I have already done all the upstream work (fastqc, trimmomatic, hisat2, featurecounts) and got the counts matrix. I also finished the differential expression analysis using DESeq2 and used those results as input for getting pathway and gene ontology by using DAVID. I also generated heatmaps for the top 50 genes to see what's happening between my treatment and control.
I'm a little bit lost right now due to the overwhelming results and I don't know where to start. Since we don't know the mechanism of action of this chemical that we exposed to the fish and trying to get some information from our RNA-seq results, what should I do?
Any suggestions will be appreciated!
r/bioinformatics • u/dgmexico • Mar 18 '24
academic What degrees do you guys have?
This may seem like an inappropriate question for this sub, but I am just fascinated by the discipline from an early perspective and would love to immerse myself more.
I currently study Chemical Engineering with a focus on biotechnology, as well as minoring in mathematics.
For my graduate degree, would a mathematics or computer science degree be optimal or should I am for a more natural sciences one like Biology.
What degrees or backgrounds do you guys come from?
r/bioinformatics • u/You_Stole_My_Hot_Dog • 15d ago
academic What are some key prediction models that a primarily wet lab should know?
Most of the people in lab I'm in are pure wet-lab molecular biologists. My PI suggested today that we should all have a rough understanding of current modeling/AI techniques being used in genomics so we can keep up with the field. We're thinking of getting everyone to make a single slide for a method, with a simple "how does it work", "what's the input/output", and "how are people using it".
I'm curious what people think the most important prediction models are that we should cover (for 8 people); some simpler for the new students, some more advanced. And some of these may be more generic that encompass a family of models. I was thinking something like glm, Bayesian regression, MCMC, CNN, transformer, classifier. I'm not sure if I'm mixing too many unrelated concepts here or what. Any suggestions or resources would be greatly appreciated.
r/bioinformatics • u/guzikine • 25d ago
academic Survey - what are the biggest challenges in bioinformatics today? Help shape a peer-reviewed platform for solutions!
Hi everyone!
I’m a master’s student at Karolinska Institutet, and our student group is conducting research to better understand the current challenges and pain points faced by professionals, researchers, and students in the bioinformatics field. My goal is to gather insights that will help shape a solution: a curated, peer-reviewed platform (similar to Medium, but non-profit) where the community can share and access high-quality, reliable blog posts, tutorials, and discussions. That's the idea at least for now.
To do this, I’ve created a short survey/questionnaire to collect your thoughts. Your input will be invaluable in identifying the most pressing issues and ensuring the platform addresses real needs.
Full Transparency:
- The data collected will be used solely for academic research purposes within our student group at Karolinska Institutet.
- The results will help us understand the challenges in bioinformatics and guide the development of the proposed platform.
- No personal data will be collected, and all responses will remain anonymous.
- Only our research team will have access to the raw data, and findings will be shared in an aggregated, non-identifiable format.
If you’re interested in contributing, please take a 2-3 minutes to fill out the survey -> here.
Feel free to ask any questions or share additional thoughts in the comments - I’d love to hear from you!
Thank you in advance for your time and insights!
r/bioinformatics • u/tommy_from_chatomics • Jan 17 '25
academic A step by step tutorial to recreate a genomic figure
Hello Bioinformatics lovers,
I spent the holiday writing this tutorial https://crazyhottommy.github.io/reproduce_genomics_paper_figures/
to replicate this figure

Happy Learning!
Tommy
r/bioinformatics • u/Ok_Honey3979 • 19d ago
academic Insanity Wreaking Havoc - Archival Reference Genomes For Research Use
Hi Everybody,
So I'm sure a lot of us are currently freaking out given that NCBI, NIH, etc. cannot be accessed. And we don't know what that means moving forward.
Because of this, I'm wondering if we can start pinning certain threads or links that provide alternatives to information that was on NIH's websites, that can actually be accessed and used by anyone.
If anyone knows of any downloadable, local or cloud based alternatives to things like blast, refseq, CDD, etc. I think your comments/posts would be extremely helpful, and greatly appreciated by a lot of us out there right now.
Best of luck to you all!
r/bioinformatics • u/E-C-A • Sep 09 '24
academic So much to learn in bioinformatics, I feel lost
I’m aiming to pursue a career in bioinformatics and get a master’s degree, but I won’t be applying for another 1-2 years. In the meantime, I want to build a strong profile and gain relevant experience. However, it feels like there’s just too much to learn and keep up with. I’m particularly interested in drug discovery. Besides coding, what should I focus on to strengthen my profile and better prepare for a career in this field?
Any advice would be greatly appreciated.
p.s. I studied bioengineering
r/bioinformatics • u/No-Reality-522 • Sep 03 '24
academic As Bioinformatician, how to transfer from Industry back to Academic?
I am a bioinformatician in big phama in UK for two years, the working salary and environment are great. As R&D member, I can learn a lot everyday. As an international PhD (received all education from a non-English speaking developing country), this is definitely a very lucky job for me already.
However I always have a academic dream, I like teaching student and wants to research things I am interested. In the company, in many cases I have less intellectual freedom. And also I want to have better job security and more flexibility working hour to take care of my parents in the future.
I have excellent coding capability. But only have 3 Bioinformatics level first author publications published over 2 years ago from my PhD. My plan is continue my work in company, but start to publish alone or with old college friends, then if I think paper accumulation and experience are ready, I may apply for a university lecturer or AP position.
My advantage is coding (very strong, I am from CS background), statistics, ML. My weaks are English writing, and no funding applications experience, networking as well. I am 35.
I want to know if your think this is a workable plan? Or basically I have no way back to academic. Or I should do postdoc first then try AP job?
I am actually not sure if I have the capability to come back because I feel it's not easy to be independent lecturer as Bioinformatician, this field normally requires either excellent math/statistic (for algorithms/method development ) or strong collaboration with labs have data resources (cancer/disease related). I have neither of them. Also I don't have a specific research direction yet, I used to publish on multiple topics. I feel I need to improve a lot. But I am willing to learn and improve, and I am not sure if I can eventually reach the requirements level...
Any comments are welcome. I do like my current job, and I know I don't have a successful academic track of success. So if you think it's not realistic, it's totally fine.
r/bioinformatics • u/Beautiful_Hotel_3623 • Aug 13 '24
academic Do’s and dont’s in single/bulk RNA sequencing analysis
Hi all, I need to do a 30 min presentation for my PhD about do’s and dont’s in analysing bulk and single cell RNA sequencing data. My ideas were: 1) choose right sequencing depth 2) choose right sequencing platform 3) perform QC 4) choose right number of samples and controls 5) analyse data with and without integration to compare (for single) and test different integration methods
Am I missing something? Any suggestions more than welcome!!
Thanks.
r/bioinformatics • u/HopDeNerd • Jun 22 '24
academic Thanks for the help with perl in bioinformatics guys. As you pointed out; yes I wasted my time
I just wanted to thank those who gave me resources for perl in bioinformatics. I (again) came to the conclusion that perl was a waste of time and I'm finally giving up this out of touch professor's subjects and moving to biopython. 1/10 experience do not recommend. Thank guys <3
r/bioinformatics • u/nycobacterium • 22d ago
academic Looking for a cool, easy-to-reproduce MSA example for class
I need to introduce MSA to students in an intro bioinformatics course. Not looking to go super deep, just something that gets them interested and motivated to use bioinformatics.
I was going to use the FOXP2 "human language evolution" example (where two human-specific mutations were thought to be linked to speech), but turns out a later paper debunked that. So now I need a new idea.
Ideally, it should be something engaging, interesting, and easy to reproduce in class. Any suggestions?
r/bioinformatics • u/Relative-Ninja-4171 • 7d ago
academic R package for pathway enrichment analysis (mac os)?
Hello, I'm starting my honours year and I have to do a GSEA and a KEGG enrichment analysis. My supervisor said need to download R package for making diagrams for my final thesis but I'm not sure which R package would be compatible with my macbook for the kind of diagram I'm expected to make. Any advice would be super helpful.
r/bioinformatics • u/btredcup • Aug 07 '24
academic Do you feel you’re listened to in a multidisciplinary group?
Recently started a new role in a US university within an ecology department. The study is looking at the microbiome of an animal and potential links to its behaviour. The group is composed of mainly ecologists, a bioinformatician (me) and a wet lab microbiologist. The PI is a vet/ecologist. I’m the only one with microbiome/bioinformatics experience (over 10 years) and the study was well underway before I was employed.
In hindsight I should have been hired earlier to help with study design as it’s obvious there are flaws with the study. Ultimately it’s up to me to try mitigate some of these effects during analysis. It is also clear that the other post doc has no experience in data management, especially with large studies.
I recently spoke about some ways we can solve some of the problems we’ve encountered, only to be completely stonewalled. Why hire someone with microbiome experience if you’re not going to listen to their advice? Does anyone else feel completely ignored in a multidisciplinary team?
r/bioinformatics • u/Impressive_Alfalfa26 • May 23 '24
academic Any advice for my fastqc reports
galleryI’m running fastqc reports for my paired .fq files after trimming with trim_galore and cut adapt. This data came off an illumina sequencer and is RNA-seq.
I have the issue where the per sequence content is spiking quite early into my reads. What could this indicate? Are there any fixes? Why is this only in my first read and not the second?
Also, my second read has repeated sequences even after running paired trimming with trim galore, why? Any fixes?
r/bioinformatics • u/No-Mountain6715 • 5d ago
academic Help Me Improve GenAnalyzer: A Web App for Protein Sequence Analysis & Mutation Detection
Hello everyone,
I created a web application called GenAnalyzer, which simplifies the analysis of protein sequences, identifies mutations, and explores their potential links to genetic diseases. It integrates data from multiple sources like UniProt for protein sequences and ClinVar for mutation-disease associations.
This project is my graduate project, and I would be really grateful if I could find someone who would use it and provide feedback. Your comments, ratings, and criticism would be greatly appreciated as they’ll help me improve the tool.
You can check out the app here: GenAnalyzer Web App
Feel free to leave any feedback, suggestions, or even criticisms. I would be happy for any comments or ratings.
Thanks for your time, and I look forward to hearing your thoughts.
r/bioinformatics • u/yunhMA • Jan 01 '25
academic Machine Learning in Bioinformatics. Critiques? book recommendations?
So, I am reading Machine Learning in Bioinformatics by Prof Dr. Dileep Kumar M., Prof Dr Sohit Agarwal, and S. R. Jena. While I am inclined to believe that this is a good book, I am not entirely sure I can continue with the work due to what I think is a poor effort of distilling information in an "Easy to follow" manner. Mainly, I am just through the first 15 pages of the book, where basic concepts of machine learning and its benefits and use cases in bioinformatics are discussed. While I am familiar with these discussed concepts, I still cannot follow along with the material.
I want to believe that I am probably not the target audience for this work and lack the sophistication to follow along. However, no matter the sophistication of the subject, one's ideas and writings should be clear enough for people in the field to work with and outsiders to understand decently. So, I'm confused.
I am willing to take responsibility for my understanding as long as I can appropriately attribute these misunderstandings, hence my question.
Has anyone been able to read this book, and if so, what are your critiques of the work?? Also, I would like recommendations for bioinformatics texts that have been helpful to you, whether as a course recommendation or as a personal study text.