Running cell ranger 1. Working with publicly available datasets and how to fetch FASTQ files For publicly available single-cell RNA-seq datasets, the raw sequencing files are often stored in SRA format on sites like NCBI GEO. Before running Cell Ranger, these SRA files need to be downloaded and converted into FASTQ files. Lets take GSE249131 for example. It opens to the GEO dataset page. scroll down to see SRA Run Selector. You are led into a page like this. What this is, is the entire raw data of the samples in the dataset. This data has 66 samples on the whole.

With every day and with every meal I cook, I dont expect it to come out perfectly. Actually the word perfect in terms of cooking has totally changed its meaning for me. Its no more having the perfect salt or spice or sweetness to anything I make, its cooking to amma’s perfection. I want every meal I make to taste like how my amma would make it. Gone are the days where I want to eat out, try a different cusine, Now, all I want is to recreate the taste of home, my Amma’s food. The first time I moved out of my house for my masters was in 2019.

I recently graduated from NYU with a master’s in Biomedical Informatics. This past year has been life changing in so many ways. This is not a post about the program or the course in NYU its about how I met the best mentors who helped me in ways I thought I didnt need help. I was a part of two biomedical research labs. The fenyo lab - purely computational focussing on gynecologic oncology The Lionnet lab - an imaging lab that is interested in understanding gene expression David Fenyö, my first mentor is the kind that believes in free will (or so I think).

The past 6 months I have been been learning something new which is single cell transcriptomics. Which is also a method I used in my master thesis. Its quite a complex topic but an extremely interesting one. I am absolutely fascinated and falling in love with. However, while starting I could not get a single tutorial that could help me get started and understand the basics. So, this is my attempt to make a getting started tutorial for absolute beginners. Introduction What is single-cell analysis? As the name suggests, it’s literally analysing single cells. In biology, cells divide and replicate their genetic material (DNA and RNA).

A couple of days ago, I attended a Women in Science and Medicine event at NYU. I initially thought it would be more of a research and networking event, but it turned out to be something much more inspiring. The panel featured amazing women doctors and researchers who have accomplished incredible things. Rather than focusing solely on research, it was a light yet deeply personal discussion about what it means to be a woman in a patriarchal society. Growing up in a gender-neutral household, I never felt disadvantaged for being born a girl. For that, I am grateful to my mother and father.

The cells in our body, communicate with each other. This is done by means of signalling. Each cell sends out signals for either communication within the cell (autocrine) or with other cells (paracrine). How are these cells released and received? The signals secreted by the cells are called ligands, which are small molecules which find its way to other cells. All cells express receptors which are protein molecules. The ligand attaches itself to the receptors and change the structure of the receptor. The function of the ligand can vary. It can be activators, inhibitors, signalling receptor, and neurotransmitters. CellPhoneDB is a repository of ligand-receptor interacting pairs.

If anything is too big to fit in somewhere, what we all do is find ways to some how accomodate it as much as possible. Maybe sugar in a storage box, grocery in shopping bags or even free food. We either split them in different boxes or stuff them in a single container. Maximizing yield. A way for computers to work with huge files is different file formats. Which compresses the file size while also maintaining the content within. Similary, when dealing with large datasets one needs to accomodate all the data points. thousands, even millions to get the maximum value of it.

Something from the book I am reading currently- Song of the cell, made so much sense so, I wanted to record it here. The author talks about “great silences” between discoveries; specifically one after the discovery of the gene. Years of silence because everyone is trying to understand and work around the new discovery(s). Streams and valley may seem to be still but, really zoomed in they are flowing. I’d like to apply this to life. Day in day out might seem like you are not doing much. But, take a moment to step back and look at the things you are doing, its work everyday.

I got to handle HeLa cells during my undergradute, the most controversial human cell line. Ever since then, I’ve been wanting to know the history behind the cells. The immortal life of Henrietta Lacks is by far one of the most powerful, content rich books I’ve ever read in my life. I regret not reading it earlier. HeLa cells are the first ever human cancer cell line. What makes them so great is their ability to divide indefinitely outside the human body. They came form the cervical cancer of a person named Henrietta Lacks. HeLa cells were vital in so many important discoveries such as polio vaccine, telomerase, HPV linked to cervical cancer few of many.

By definition, Agent-Based Models (ABM) are small-scale computational models used to simulate the actions and interactions of agents, which may represent individuals or groups. Imagine you are a graduate researcher studying Drosophila as your model organism. To support their survival, you need to prepare a culture medium and test the effects of different variables—say, for example, how different concentrations of perfumes impact Drosophila growth. However, you’re unsure of the exact outcomes and don’t have the time to conduct multiple rounds of experiments. You want to achieve optimal results on your first attempt. This is where ABM can be useful. In this case, the Drosophila would be the agents in your model, and the culture medium would be the environment you’re trying to simulate.