BatchX User Insights: Alberto Gonzalez

We plan to write a series of blog posts called BatchX User Insights, outlining how BatchX is being used on the field by experts like Alberto. In this case, a glimpse to show how BatchX can be more than just a platform to process data but an instrument to accelerate clinical research and save lives.

Alberto is a postdoctoral researcher at the Vall d’Hebron Institute of Oncology ( VHIO) in the Cancer Genomics Group. His research group works on genetic screening of cancer patients by identifying genomic mutations and gene expression alterations that will determine the patient’s eligibility to be enrolled in phase I clinical trials. Alberto, along with rest of the Cancer Genomics Group, continues to push frontiers of cancer research with their latest work, involving a much more robust cancer profiling method. He is part of the team responsible for designing, testing, and validating the techniques that are being used to analyze the tumor samples. We recently interviewed him about how BatchX is working out for him and it seems it has been a transformative experience.

Considering your objectives at VHIO, is BatchX helping you in this process? In that case, where does BatchX intervene?

Of course, BatchX is being very helpful in this process. It has helped me run the bioinformatics analyses needed to process the raw data generated by the sequencing platforms and obtain the results I need.

So far I have been using BatchX to perform RNA-Seq analyses, which is one of the NGS derived techniques we use to identify oncogenic gene fusions and gene expression alterations, both of which play an important role in the diagnosis and the treatment of cancers.

How has BatchX changed your usual workflow? Was there something that you were completely unaware of before you used BatchX?

Before I started using BatchX, I was completely uninvolved in the bioinformatics analyses of my samples and depended 100% on the bioinformatics personnel from our lab to do this. Now, even though I still require their assistance, I have gained a lot of control and autonomy to perform my own studies. This has also helped me to better understand the analytical procedure as a whole and identify critical steps on the process that can be tuned to improve the quality of my results.

Explain the new things that you had to learn when integrating BatchX in your workflow. Has your productivity improved after using BatchX?

“Before BatchX I completely relied on somebody else to perform these analyses for me.”

I had no previous experience in bioinformatics, so I had to learn a couple of things, like basic Linux commands in order to manage my data and launch my workflow analysis. From a bioinformatics standpoint, the amount of time to get results has been reduced significantly. As I said, before BatchX I completely relied on somebody else to perform these analyses for me. So the waiting time depended on their availability and the amount of work they had on their desk. Sometimes, that meant waiting a few weeks before having the results for my RNA-Seq studies. Now, I’m in control, it’s on me. I can have those results on the same day if I need them.

I do have to say though, that it wouldn’t have been that easy if I hadn’t had the support that the BatchX team has provided me. They assisted me through the process of familiarizing myself with the platform and helped me in the development of the pipelines I needed.

“Sometimes, that meant waiting a few weeks before having the results for my RNA-Seq studies. Now, I’m in control.”

Do you feel your whole team is benefiting from BatchX or is it just your life that is easier now? Do your team members share a similar profile as yours?

In my team, I must be the one who has used it extensively, but I know BatchX has helped my teammates in other types of analyses that are different from RNA-Seq. Some of my team members are experienced bioinformaticians who have also found BatchX useful for their own specific needs.

How much time do you think you would have spent extra if you didn’t get to use BatchX

In my case, having to process this huge data by myself would have been “non-viable” if I hadn’t had BatchX.

How much time of your day is spent on BatchX these days?

Time spent is very variable, it depends on the samples I have to process, which can range from 0 hours for those days when there are no samples scheduled to be analyzed to a few hours if I have a great demand.

During the Covid-19 lockdown, for example, when I didn’t have access to the lab and had to stay at home, I invested a lot of time in learning the BatchX platform, testing different programs, pipeline configurations and re-analyzing samples.

How many new jobs do you foresee migrating to BatchX within next month? Next year?

At Cancer Genomics we are committed to delivering a more personalized medicine for patients suffering this disease, our objective is to translate advances in molecular research to patient care as rapidly as possible, so we are expecting to analyze hundreds of tumor samples in the following months, this will bring us closer to optimizing patient stratification and identify more effective targeted therapies for individual patients. RNA-Seq is one of the techniques we rely on to achieve this, so I’m looking forward to using BatchX for these analyses.

“We are expecting to analyze hundreds of tumor samples in the following months”

Name one problem you weren’t able to work around before using BatchX. Be specific.

Basically any bioinformatics analysis I had to perform by myself.

Let me add that I’m not alone in this situation, there are many researchers out there with very little or no bioinformatics experience, who haven’t found the right tools to process their own data and at the pace they would want to. I’m actually lucky for having an excellent bioinformatics team as part of our research group, however there are many other laboratories with no bioinformaticians in their group, which makes their situation much more complicated.

How would you feel if you could no longer use BatchX?

There are many feelings coming to my mind right now: frustration, disappointment, annoyance. Just to name a few.

Originally published at https://blog.batchx.io on August 17, 2020.