Wednesday, July 29, 2015

Singapore, Day 3

It was hard going this morning for the biologists, as there were three main computational talks. First, Vince Moulton further developed some of his ideas about split networks, including median networks, quasi-median networks and neighbor-nets, and what sorts of trees they might contain. Then, Céline Scornavacca expanded on her ideas for calculating the "hybrid number". Finally, Jens Lagergren outlined his work on fitting gene trees to known species trees and networks; this has come a long way in recent years.

We had the afternoon off, although many people took the opportunity to pretend that they were still in their offices at home. Myself, I sat by the pool waiting for the temperature to cool (this was the hottest day so far this week), and then went to the Singapore Botanical Gardens, where I circumnavigated the Evolution Garden, the National Orchid Garden, and the Rainforest Walk. I then briefly perused Orchard Street (one of the most ridiculous shopping meccas you will ever see) and the Raffles Hotel (an even more ridiculous hang-over from British imperialism), before returning to the pool side. It's a tough life.

Tuesday, July 28, 2015

Singapore, Day 2

The computational people were very patient today, as the three major talks focussed on biology, with only the shorter talks being computational.

In particular, Eric Bapteste and James McInerney were determined to tackle the true complexity of phylogenetics, rather than trying to see genealogical history as being a tree with reticulations. They have recently been championing sequence similarity networks as tools for exploring phylogenetic history, and Eric discussed them in relation to prokaryote evolution while James looked at gene families. Strictly speaking, SSNs are not phylogenetic networks, because they do not involve the inference of unobserved nodes connected to observed (labelled) nodes by inferred edges, bit instead connect observed (labelled) nodes via observed edges. This does not mean that they have no role to play in phylogenetics, as the speakers made amply clear.

My own talk had little to do directly with empirical networks, but instead tried to look at an overview of the field, presenting some of my own ideas about where networks are heading, and what role they might play as phylogenetic tools. Not everyone was convinced.

Also of personal interest to me, Philippe Gambette unveiled the new, much more ambitious, version of the Who is Who in Phylogenetic Networks database. I claim no other role in this than encouraging Philippe to be as ambitious as possible. I think that people will be genuinely impressed by what can now be done to explore the people, literature and software associated with phylogenetic networks.

PDF copies of the talks have now started to appear on the workshop web page, which will give you a bit more idea of what our speakers have tried to say.

We also started the discussion about how to engender more effective development of computational tools for phylogenetic networks. Topics covered included the need for more gold-standard datasets that can be used to test new methods — to date, the ones available on this blog have been compiled by me alone, but in order to expand this other people will need to contribute. Also, improved communication and collaboration between biologists and computationalists would be very helpful, and several suggestions were canvassed, but no real way forward was found. One interesting point was made that many of the practical applications of networks were not likely to attract the professional interest of most computationalists — indeed, to date, most phylogenetics programs have been written by biologists rather than computational people.

In the evening, I had a very enjoyable dinner at the Singapore Seafood Republic, in the company of Louxin Zhang (our organizer) and some very nice Chinese visitors, all of whom politely failed to comment on my inability to use chopsticks. Pictures of dinner were taken, and may appear on Facebook, if I am not careful. We finished just in time to watch the Sentosa Crane Dance, which you should all check out.