Tag Archives: Developer

On the line: 13 questions for Thomas Hrabe, serial research tool developer

Today’s On the line is with Thomas Hrabe, a talented postdoc from the Godzik lab at the SBP Medical Discovery Institute, La Jolla, with a special interest in the structural biology of the nano machines that run this whole operation we call life, i.e proteins.

Thomas has developed several important tools in the field of molecular structure analysis, ranging from trendsetting electron tomography processing with PyTom, to scientifically insightful tools such as PDBFlex. Additionally, Thomas has contributed to the development of Cancer3D, a tool to track drug sensitive and driver mutations, and which he may soon proudly say made the transition from the bench to the bedside.

But let’s not give away any more spoilers, let’s hear it directly from the source. Thomas, take it away!

Continue reading On the line: 13 questions for Thomas Hrabe, serial research tool developer

Network-of-Cancer-Genes

On the line: Interview with the three musketeers behind the NCG tool

 This time we are on the line with Giovanni Marco Dall’Olio, Thanos Mourkis and Omer An bioinformaticians who developed the Network of Cancer Genes.

NCG is a web resource to analyze duplicability, orthology, and network properties of cancer genes. Manually curated, it introduces a more robust procedure to extract genes from published cancer mutational screenings. NCG wasn’t just developed to scratch a curiosity itch. In fact, Omer utilized this powerful tool to uncover fascinating biological insights throughout his research.

Continue reading On the line: Interview with the three musketeers behind the NCG tool

cell-where

On the line: Interview with William Duddy creator of CellWhere

On the line this time around is William Duddy, from The Pierre and Marie Curie University, who focuses on making sense of omics data in neuromuscular diseases. With the tragic loss of his brother to Duchenne muscular dystrophy, William is particularly interested in advancing our knowledge about this terrible disease.

Staying closely involved with wet-lab biologists, William discovered the need to associate gene networks to subcellular locations. This led to the development of CellWhere, a tool that structures omic data and is aimed to help anyone that feels lost when viewing a protein-protein interaction network.

Now let’s dive into hear the behind the scenes story of CellWhere and its creator.

Continue reading On the line: Interview with William Duddy creator of CellWhere

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.

Continue reading On the line: Interview with Camelia Quek iSRAP developer