This weekend (Jan 9 - Jan 10), I participated in a workshop on mathematical and computational biology (WMCB-2016) organized at Indian Institute of Science Education and Research Kolkata (IISER-K). This annual workshop is co-sponsored by NNMCB, a group of multiple premier institutions in India that coordinate activities in the area of interest.

The primary motivation for participating in this workshop was to present my ongoing work on the knotted proteins. It seemed like a reasonable place to attract further ideas and help. Sadly, I could not get in touch with my advisor before the abstract submission deadline and did not submit a poster. Nevertheless, it was fun to listen to new speakers and learn about new developments in the field. You never know where ideas can come from.

The workshop consisted of 8 invited lectures, 6 short talks combined with a poster session spanning over two days. There were no hands on or practical sessions even though the event was called a workshop. I guess it is because of the short talks, a 15-minute presentation given by Ph.D. students as about their work.

Venue

IISER-K is located about 50 km from Kolkata, the nearest metropolitan and also my home city. Located in a countryside with almost nothing around, the new Mohanpur campus of IISER-K stands proudly with its large and lush green beauty. Although, a few of buildings are still under construction, the place will soon become a buzzing center of education and research in India.

Talks

The complete list of research talks, short talks, the list of posters can be found on the website. Below, I’ll talk in brief about my impression of the workshop along with short descriptions as necessary.

Complex systems and networks

There has been growing interest in modeling and analysis of complex biological networks in the past decade. (Barabasi et al.) Primarily because advancement in data acquisition platforms has enabled us to generate a huge amount of omics data - genomics, transcriptomics, proteomics, metabolomics, fluxomics to name a few. The variety and complexity of data has attracted specialized knowledge of different scientific domains, especially inter-disciplinary participation from physics and mathematics.

Sarika Jalan heads the Complex Systems Lab at Indian Institute of Technology Indore. She is trying to create a universal framework for a generalized analysis of protein-protein interaction data from diseased cells. It will allow one to easily identify key players that cause transition from normal to the cancerous stage.

Later, Indrani Bose, an eminent senior physicist at Bose Institute provided a hardcore illustration of the cells as complex systems by expanding on the topic of cell differentiation. The talk was dense but the key idea was to convey the importance of noise and heterogeneity in the cellular system as an important component of the decision making including cell differentiation. I will list a couple of interesting papers she suggested for more information.

Big data analysis

It should no longer be surprising that a computational biology workshop involves a large number of talks on big data analysis or multi-omics integration. The talks by Saumyadipta Pyne (IIPH Hyderabad) and Krishna Prasad (IIT Gandhinagar) focused on acquisition and analysis of high dimensional data either from single cell analysis or neuroimaging data. In these cases, often the breakthrough is in creating a new model that describes your data instead of trying to reduce its complexity.

Computational protein design

Pralay Mitra gave an interesting talk outlining a general computational strategy of protein design. For those who are unfamiliar, protein design is an inverse problem of protein folding, wherein you start from a known structure and its sequence and work out alternative sequences. The motivation for this problem is rather subtle as to why would anyone want to have a different sequence for the same structure. And if different, why not just carry out a single mutagenesis. The central idea, however, is not to generate just a different sequence but a novel sequence with strikingly different properties of interest. For example, we may want a protein structure with same sequence but different affinity so that it acts as an inhibitor. A reverse engineering problem. One may also notice that protein design problem inherently involves a protein folding problem as well.

But how do you do it? Perhaps, I will write about it in detail in my other posts.

Mechanical organization of cell

The talks by Anirban Sain (IIT Bombay) and Ranjith Padinhateeri (IIT Bombay) aimed to understand the mechanical organization of a cell. How does the dynamics of cytoskeletal filaments drive shape transformation, cell division and other processes that require force generation and modulation?

A good part about these talks were the pretty electron microscopy pictures they show.

Short talks and Posters

Several short talks and posters by Ph.D. students were presented. Different concepts like game theory, protein-protein interaction networks, molecular dynamics simulation, spectral graph theory, and neuroscience came up in the discussion.

Other

Some relevant techniques (or terms) that I wish to read upon and explore further are:

  • Replica Exchange Molecular Dynamics (REMD)
  • Riboswitch Scanner Tool
  • Molecular Dynamics tools - Amber12, Chimera tool etc.
  • Studying transient dynamics, Langevin equations

Possibly in my undergraduate thesis itself.

Criticism

One fact that disappoints me slightly is that most of the researchers do not really care about experimental evidence in support of the theory or analysis they put forward—or if they do, do not have a plan about it. The general attitude is, “We’re done. It is now up to others to build on this work and validate.

We need more collaborations.

Overall, a good workshop to spend the weekend. I am glad to have made a company of like minded people as well.

blog by Vivek Rai