Cameilia Quek

On the line: Interview with Camelia Quek iSRAP developer

On the Line

This time we are on the line with Camelia Quek, an experimental biologist with computational skills whose main research focus is understanding the (early) mechanism of disease.

Camelia has developed the iSRAP online tool that performs comprehensive analysis of small non-coding RNAs by generating different visual representations of digital data. iSRAP has the potential to serve as a platform for rapid analysis of transcriptomic data, so better informed decisions can be made on the downstream analysis.

Let’s get to it.

Camelia, welcome to On the Line with LabWorm. Before we dive into the iSRAP, could you tell us a bit about your field of research?

I have great interest in human infectious pathogens. The dynamic interplay between host and pathogen has always been my favorite topic.

Prior to the manifestation of clinical symptoms, the biological system gets perturbed. In order to understand the pathophysiological aspect of diseases, I use experimental and computational methods to unravel the interaction between host and pathogen (or infectious material) at different disease stages.

What makes the iSRAP, which you developed, better than similar existing tools?

First, better time management. The automated feature of iSRAP allows researchers to focus on interpretation of biological meaning. There are no requirements to re-format the raw sequencing data as standard FASTQ, and BAM format are accepted for data processing. The configuration file provides concise information for running the pipeline, allowing the record of analysis details for future downstream work.  The manual preparations of file formats are eliminated by a single command.

“iSRAP allows researchers to focus on interpretation of biological meaning”

Second, high-throughput capability. Numerous sequencing samples for data analysis are executed by parallel processing in iSRAP. Unlike web-based or GUI-based tools, there are no limitations on the sample file size or uploading time.

And visual representation of data. Meaning, to allow complex digital information to be presented quickly and clearly, so biological relationships can be explored and interpreted.

What were some of the tools you found most useful developing yours?

Trimmomatic, Bowtie2, SAMtools, FastQC, RNA-SeQC, BEDTools, DESeq, edgeR, and Voom.

Did you collaborate with anyone on the development of iSRAP?

Yes. We collaborated with VLSCI in Melbourne and it proved to be a very important aspect in developing iSRAP. VLSCI provided us with excellent facilities and their researchers were top-notch and very helpful. The collective attributes of VLSCI have brought the pipeline forward and sped up the progress of development.  

You didn’t just submit your tool to a repository, but went on to build a dedicated website for iSRAP. What were your considerations in doing that?

Based on my experience, a repository web interface may be unfamiliar to (experimental) biologists, resulting in them moving away from stand-alone analysis tools. So the main objective of the iSRAP website was to reach out to experimental biologists, as well as bioinformaticians, and to provide a means of communication to connect more people in the scientific community.

What were some of the challenges you faced while developing iSRAP?

As I was initially trained as a scientist who has little computer science/bioinformatics/statistics background, I faced many challenges along the way.  I often find myself wrestling with problems such as proper usage of codes, syntax issues and indexing errors.  I also find it incredibly difficult to write down the codes based on my logics.  Despite of all these challenges, I definitely find it very rewarding to finish a script that enables the completion of desired tasks.

Do you have any words of wisdom to starting computational biologists out there who want to develop their own research tool?

“Despite of all these challenges, I definitely find it very rewarding to finish a script”

This would be best summarized in one of my favorite quotes from Steve Jobs: “Your time is limited, so don’t waste it living someone else’s life. Don’t be trapped by dogma – which is living with the results of other people’s thinking. Don’t let the noise of other’s opinions drown out your own inner voice. And most important, have the courage to follow your heart and intuition. They somehow already know what you truly want to become. Everything else is secondary”.

What are the top sites / resources you most often use?

RNA-Seq blog, Broad Institute GATK, VLSCI,  Bioconductor and R.

Camelia’s Toolbox (click to view the full Toolbox)

Let’s talk LabWorm for a sec. Is the possibility to see what resources other researchers are using appealing to you? And would you share your toolbox – your tools of choice – with other researchers?

In order to keep up with technologies and tools in this fast-paced environment, it is very important to discuss and exchange knowledge and share tools experience. By following researchers, and sharing tools with them, it will assist everyone, researchers and students alike, to speed up their work.

Looking ahead, what are your aspirations?

“Following researchers and sharing tools with them will assist everyone to speed up their work”

I want to specialise in the informatics aspect of my research, and to continue applying and improving my computational analysis skill upon my biology knowledge. My ambition is to inspire and nurture the next-generation scientists on inter-disciplinary science.

This isn’t the Oscars, or the MTV music awards, but do you have someone you would like to thank that contributed to your research?

I would like to express my heartfelt thanks to Dr. Chol-hee Jung. I had a rough start to my PhD due to my inter-disciplinary background, and his patience, advices, and guidance were very much appreciated.

Thanks for taking the time to chat with us Camelia, and may the Worm be with you!

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