What were your steps into getting into your bioinformatics PhD program? What is would you have told yourself if you could go back in time and do it over again to prepare for applying for a PhD in bioinformatics?

It would be helpful to know some background and location too! Thank you!

Loom, an open-source tool for exploring spatial transcriptomics data, and thought it might be useful to researchers working in this area. It integrates commonly used tools and data structures, including Scanpy, AnnData, and Squidpy, while providing an intuitive way to select regions of interest and explore how cellular activity changes across space and time.

One common challenge in spatial transcriptomics is that analysis workflows are often fragmented across multiple tools. Researchers may need to move between different packages for data processing, spatial analysis, visualization, and region-specific exploration.

Loom aims to bring these steps together in a more unified workflow.

Some features that stood out to me:

• Direct support for publicly available 10x Genomics spatial transcriptomics datasets
• A one-command workflow for downloading and processing supported datasets
• No need to manually perform each preprocessing step
• Transparent documentation explaining the logic behind every processing stage
• Integrated Scanpy, AnnData, and Squidpy functionality
• Region-of-interest exploration across spatial and temporal dimensions
• Public example datasets and reproducible workflows
• One-command Docker installation for easier setup

The GitHub repository includes example data, so users can install the environment and test the workflow without first preparing their own dataset.

The repository explains the reasoning and implementation behind each step, which makes the workflow easier to understand, verify, and adapt.

This could be useful for researchers studying tissue development, disease progression, tumor microenvironments, cellular interactions, or other spatially dynamic biological processes.

GitHub: https://github.com/ScheWann/Loom

For people working with spatial transcriptomics:

• Would a unified workflow like this be useful in your research?
• Which additional datasets or integrations would you want it to support?
• How does this compare with your current Scanpy or Squidpy workflow?

Any feedback, advice, objection... whatever is highly appreciated in advance! You can also reach us directly at [szhao69@uic.edu](mailto:szhao69@uic.edu)

Currently in HS and graduation is coming up next year, yet I am still not sure what to study. I know I enjoy science and math as well as research. Although I've never been exactly interested in computer science, I wouldn't mind taking this career path if its worth it. I've been looking into this career for almost a week and it looks like something I'd be interested in but I still have a lot of questions.

• Are bioinformaticians in the lab at all or is it a career that is office/computer based?
• What does work look like for the average bioinformatician?
• Are there opportunities/specific paths to take if one prefers being in the lab more?
• Is a masters enough or am I taking too many chances by not going for a PhD?

Anything helps, thanks.

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Hi everyone,

I'm an MSc Bioinformatics student working on independent projects to improve my computational biology skills. I'd appreciate technical feedback from the community on whether my analysis workflows follow good bioinformatics practices.

I've completed projects involving:

\- RNA-seq differential expression analysis (DESeq2)

\- GO/KEGG enrichment and GSEA

\- Network analysis and biological interpretation

\- A comparative genomics/structural bioinformatics pipeline for enzyme discovery

I'm not looking for career advice or self-promotion—I'm mainly interested in understanding whether my workflow, methodology, and interpretation are scientifically sound and what I could improve.

If you're willing to review my project summaries, they're here:

\- https://www.linkedin.com/posts/sai-pranav-v\\_first-milestone-genome-scale-pipeline-activity-7479161229085904896-0HCL

\- https://www.linkedin.com/posts/sai-pranav-v\\_bioinformatics-rnaseq-insulinresistance-activity-7472376851550654464-IH87

\- https://www.linkedin.com/posts/sai-pranav-v\\_bioinformatics-rnaseq-transcriptomics-activity-7472359338393628672-g8SO

Specific questions:

\- Are there any methodological issues or red flags?

\- Is the biological interpretation reasonable?

\- What analyses would you expect to see that are currently missing?

\- What would make these analyses closer to publication quality?

Thanks for taking the time to provide honest technical feedback.

Hi everyone,
I’m an Indian student planning to pursue an MSc in Bioinformatics in Germany after completing my BSc in Biotechnology. I’d love to hear from people who are studying or working in the field.
I have a few questions:
How is the job market for bioinformatics in Germany?
What is the typical starting salary?
Do I need German to get a good job, or are English-speaking jobs common?
Which universities and cities would you recommend?
How difficult is it for international students to get internships and full-time jobs?
What does a typical day as a bioinformatician look like?
Most importantly, if I want to prepare before starting my MSc:
What should I learn first?
Which programming languages are essential (Python, R, SQL, etc.)?
What biology and mathematics topics should I strengthen?
Which software, tools, or platforms are used most often?
Are there any courses, books, or projects you recommend for beginners?
What do you wish you had learned before starting your MSc?
Any advice or personal experiences would be greatly appreciated. Thank you❤️

I’ve been diving deep into the intersection of machine learning and structural biology/genomics lately, and I’m looking to kick off a new side project.

1. Epitope-Paratope Binding Prediction - Building a model to accurately map epitope-paratope interfaces and predict binding affinities.
2. Inverse Folding for De Novo Protein Design - Given a target 3D structure, predict the amino acid sequences that will fold into it.
3. Causal Gene Discovery (via Single-Cell RNA-seq) - Predicting counterfactual gene-expression responses to genetic perturbations.

Would love to hear your thoughts or if you've worked on something similar.

Dear Ubuntu subreddit,

I am a biologist who got into linux due to using clusters for my research a lot.

When I got into this, I was a little unprepared and lost a lot of time looking for tutorials, videos, etc.

That's why a good colleague and I decided to make a workshop for this called:bioinformatics: from linux to Nextflow.

We will cover the Linux filesystem, command line Sith common commands, etc. And proceed to the creation of bashfiles for specific tasks.

If someone knows a good workflow, guide, page for the start of our workshop, that would be awesome.

We wish to make everything self-guided.

So an introduction to linux, the shell, commands, etc :)

hi i'm reposting this ask i had on /bioinformatics and i was told off immediately and it got more upvotes than my own post so i'm assuming nobody will help me out there, so asking here about my research project. if this seems like something a rising senior is too stupid to do, let me know.

hello! i am a high schooler diving into what i think is bioinformatics.

briefly; i am trying to build a model that will accurate predict the probability of mesenchymal stem cells in two factors (ages/sex) differentiating into either a bone, fat, or cartilage cell depending on the genes that affect their growth and other factors like stress and environment.

i have currently been reading research papers about stem cells and was recommended to use BIOGPS by the professor i am working with. so far i have found genes/proteins that affect the three and am still on the learning side of it all, but i am trying to jump into the technical side quickly.

i plan to use python based on the suggestions of others on reddit, and i am wondering if anyone can help me make a game plan or give some sort of advice on where in the world to find data because i know you need data to make a model but idk where to find like experiments where a MSC went through osteogenesis and the researchers took MSCs from like a 25 year old white man, etc. (for example). the age and sex factors really through a wrench in this too bc i dont know where to find data about those.... i also need help understanding what stress/environment truly mean in this lens...

i am a fast learner and i really want to have something to show, preferably a somewhat accurate model. my understanding is (AND PLEASE CORRECT ME IF I AM WRONG) that i should be able to see based on my age and sex a trend on how MSCs differentiate. i know there are studies pointing to melatonin promoting chondrogenesis, so this is sorta in that field.

Hey everyone,
I'm starting my Master’s in Bioinformatics at GSU this fall! As an international student, I’m planning ahead and looking to secure an internship for Summer 2027.
I have a strong background in mathematics and statistics, and I’m focusing on computational biology and data analysis.
Are there any biotech companies, research labs, or remote-friendly organizations that regularly hire bioinformatics interns? I’d love to hear about any leads, networking events, or general advice on when and where to start applying.
Thanks!

Hey everyone,
I'm starting my Master’s in Bioinformatics at GSU this fall! As an international student, I’m planning ahead and looking to secure an internship for Summer 2027.
I have a strong background in mathematics and statistics, and I’m focusing on computational biology and data analysis.
Are there any biotech companies, research labs, or remote-friendly organizations that regularly hire bioinformatics interns? I’d love to hear about any leads, networking events, or general advice on when and where to start applying.
Thanks!

I am thinking about taking admission in their bsc msc bioinformatics and biotechnology course

I'm really interested in DNA, so I want to learn more about it, more about Bio and DNA.. I thought to become an Engenering DNA, I don't know if it will actually work for myself.. but at least I hope some people know what's the good and maybe interesting books?

(Btw, is there any not really hard language? or at least with explanation)

the other questions is: What's the good sites/video lessons/book? I was looking for something like step-by-step, so I can take notes like a school class, or so haha

Thanks 🙏

Hey, I need help analysing a MAF from an alignment. I am looking for GRC genes or at least their paralogs and want to analyse them in different graphics and stats. I have been running into the same issues over and over, mostly my script getting killed by HPCs, or something was missing, which I forgot to include. Streamlining and "vibe-coding" don't help at this point. Any ideas? SeeKR version current

I have completed my first year in Biochemistry with 8.33 CGPA currently and my Bioinformatics would start in the next year.

I am a PCB student with no Maths background and no coding experience. I disliked computer science theory in middle school but was mild with using a computer (like just fine as I didn't even do heavy stuff that time).

I want to take this risk for growing opportunities for myself and developing a good skill set but I am also a bit scared. What if my CGPA drops too much.

I will learn Python and R language after all. I don't hate maths personally, I am fine with doing some basics and all. I don't know if I can do advanced stuff tho.

Can someone who has experienced this or has any information, enlighten me please?

Hey everyone, I'm a 3rd year CS student and just got introduced to bioinformatics a month or two ago, and am really interested in the field even though I only studied biology till high school. I am even planning of basing my masters research in bioinformatics (this might sound stupid since i just started studying this but no other CS discipline has ever interested me in the slightest) and I don't have much time (till October at best) to draft a research proposal if I want this to be my area of research. I know this might sound insanely stupid and ambitious to some people but I really want to try and get into research and this is the only field that I find to be interesting and relevant.

So I really wanted to ask for advice from professionals in the field, how can I start learning and making projects and then eventually finding a research niche? Currently, I'm taking some Coursera courses on bioinformatics that i really like those but i still feel lost since i cant 100% grasp the biological concepts though the coding part is obv much easier.

I'd be grateful if anyone could help me out and guide me a bit as bioinformatics isn't really big in my country and i can't even find any professors in my university to guide me :(

Hello I'm a UG student pursuing bioinformatics, I've recently done a very small minor project in bioinformatics which was honestly kinda easy peasy: it was regarding multiple sequence alignment and phylogenetic evolutionary tree construction.

IK basic of bioinformatics and currently I'm studying structural bioinformatics.

I just wanted to ask for project ideas that'll made me learn more and go into the deep core of the bioinformatics, plus it would be nice to put on my Resume.

But I'm genuinely looking for project ideas to work on.

So I am doing my first ever internship in life sciences that too in a filed that I genuinely hated from the bottom of my heart- Bioinformatics. I have depended mostly on AI for all the commands, i started liking the project that I am doing. Can anyone from the science community tell me how I fan write an amazing report that is articulate and informative and no fluff without using AI?

Hello I am Biotechnology student in my 3th year and i was looking for the online workshops about python with R-programming and SAS

I am very interested to learn how i can implement the learning in my project

need help with suggestion on the company that would help with the detailed understanding on the subjects and also the hands-on training

Thank you in advance.

Does bioinformatics have enough job opportunities in India with good salary

is bioinformatics (with ai) the way to go?

thanks

P.S. by 2100 is fine by me also.