Blog Posts

Latest posts covering bioinformatics methods, computational biology insights, and technology updates.

May 20, 2025 4 min read
Beyond the Pipeline: Advancing Diversity in Challenging Times

Last Friday, I had the chance to join a panel discussion on advancing diversity in challenging times. I was lucky to be joined by two brilliant next-gen scientists, Francince Camacho and Saba Nafees. Follow them—they’re going to be incredible leaders and influencers in our field and beyond.

Nov 21, 2024 2 min read
Showcase: My Quick Dive into Pipeline Automation with Seqera AI

Example of automation with miniaml investment but good results
Aug 15, 2024 2 min read
Perspective: Note directed to leadership in Biology, Translational, Chemistry and Technology.

Talk to a computational biologist scientist from the idea not the data
Feb 28, 2024 5 min read
My Learning Experience with Computational Infrastructure in Biotech/Industry

The mistakes and the success of building as fastest as possible the infrastructure
Dec 9, 2023 1 min read
3D-printer WALL-E toilet paper holder

Finally tired of the broken TP holder and how to make a trip to Home Depot a 2 months project.
Last updated on Sep 30, 2023 6 min read
My story with cancer - Jimmy fund walk Oct 1st

My personal experience with cancer and how much work still to do
Oct 3, 2019 5 min read
My transition to biotech

My personal experience giving up on academia to bet on industry
Jul 19, 2019 1 min read
kallisto-bustools 

       JobID                        JobName      NCPUS     MaxRSS     AveRSS  Elapsed
------------ ------------------------------ ---------- ---------- ---------- ----------

14150319                             index          2     91.06G          0   01:26:32

14153823                          kallisto          2     67.28G     65.34G   00:59:35

14156768                       bus-correct          4      1.19G      1.19G   00:01:29

14156812                  bus-capture-cdna          4     16.16G     10.22G   00:07:59

14156835                bus-capture-intron          4     16.27G     16.27G   00:06:54

Jul 11, 2019 5 min read
How to set up cellranger to make your hpc admin happy

I found myself to force to use cellranger. Meanwhile it helps a lot to run from bcl files to single cell counts matrixes, I discovered that is quite difficult to control many options related to optimization.

Apr 5, 2019 2 min read
How to set up public dataset analysis with bcbio-nextgen

We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set.

Inside bcbio, we have bcbio_prepare_samples.py to help to merge multiple files that belong to the same sample into one file to make easier the configuration of bcbio. We extended this script to pull down data from GEO and SRA repository.