I’ve been quiet since April, but I’ve also been pretty busy. I have been to one meeting this summer, the 20th International Congress of Arachnology. I gave a talk about the progress on the spider behavior ontology I mentioned a few posts back. The slides are here. I have finished my initial pass for behavior terms in two recent works: Foelix's Biology of Spiders, a standard textbook, and an edited volume, Herberstein's Spider Behaviour. Since returning from the meeting, I've nearly finished a first pass of data cleaning. You can see the raw data here. In the next week or so, I'll put up a little landing page with more explanation and links to the raw data and the results of the cleaning pass. Eventually there should be a CMAP or other visualization and possibly an OWL file.
I say possibly an OWL file because I'm not sure that an ontology will be the final outcome. I may generate a set of terms and turn them into term requests for the NBO/ABO, the Spider Biology Ontology, and others (GO, ChEBI, PATO). It's been clear to me (finally) that the database is where the interesting comparative work will come from and the ontology is just a necessary support for this. It should also be useful as a standardized vocabulary for arachnologists, and there seems to be interest in this, based on the reaction to my talk.
Showing posts with label Meetings. Show all posts
Showing posts with label Meetings. Show all posts
Friday, July 22, 2016
Wednesday, July 15, 2015
Models vs. Data - not a choice for behavior
These are some thoughts that have been rattling in my head since the SSB 2015 standalone meeting back in May. They are somewhat depressing, so I'm open to suggestions of more positive ways to look at the situation in comparative studies of behavior.
The main part of the meeting was bracketed by two 'panel' discussions (I scare quote the word panel because the panel was two people in each case). The first panel consisted of David Hillis and Antonis Rokas arguing whether models or data would be more important going forward. Not surprisingly for this meeting, the focus was on molecular methods, particularly genomic comparative analysis. Interesting question, but of course both are viable research paths at this point - gathering and managing rapidly growing data sets and refining the models of molecular evolution to more realistically mimic the actual processes are both worth pursuing.
The question of data vs. models came up several times, including during another panel discussion of putting dates on time trees. This seems to be a very fertile area for developing improved models and statistical methods at the moment, while the corresponding fossil data is accumulating at a steadier pace.
The second panel was Wayne Maddison and Cécile Ané discussing the limits of comparative methods. The issues that Wayne raised are ones I know firsthand, mostly from my stint in his UBC lab. The issue is that most or all comparative methods for discrete trait values suffer from phylogenetic non-independence, despite 25 year-old claims to the contrary. I spent some time thinking about these issues, but the best discussion at this point is the Maddison and FitzJohn (2014; doi:10.1093/sysbio/syu070) paper. The situation is somewhat better for continuous traits, though there are always questions of model adequacy. I'll admit I don't remember a great deal of Ané 's discussion of limits of OU methods, though it seemed someone more optimistic for the continuous trait cases that OU applies to. Wayne did point out that tip data won't help answer the question of trends in evolution - you'll need fossil data for that.
Thinking about the situation after the meeting wrapped up, I was struck about the differences between different trait domains. In molecular biology we have lots of data and a selection of models that are at least plausible representations of things that actually happen (not perfect by any means, but GTR is a reasonable stochastic approximation of what happens at a single site). Lots of data allow a certain freedom to 'run about' the non-independence problems mentioned in the last paragraph - with enough sites, you could, in principle, assume independent changes. Molecular data also provide a small, but real sampling of fossil data and useful amounts of molecular evolution can occur over experimental time-scales. Thus, molecules provide lots of data, a solid starting point for models, and some temporal depth. Morphology has fossils, a reasonable and slowly growing dataset and a mix of continuous and discrete trait models. Are Brownian motion and OU models good stochastic approximations of morphological change for continuous characters? Not necessarily, but they are definitely a start. As noted above, the situation for discrete characters, even using model-based (Likelihood and Bayesian) methods is rather problematic. However, you aren't limited in your ancestral reconstructions to using contemporary data. This won't solve these problems, but they might give you confidence in your analysis. There is room for optimism here, particularly the hope of better models and statistical methods to make the most of the data available, while new data trickle in.
Then we come to behavior: no fossil data and not a lot of data at all relative to molecular traits. Behavior also has the problem of much of the data being transient - if not captured on a recording device, it's just an observer's memory. Apart from the lost opportunities to capture data, the animal behavior community has been slow to embrace the culture of data sharing, as discussed in Caetano and Aisenberg's (2014; http://dx.doi.org/10.1016/j.anbehav.2014.09.025) Forgotten Treasures paper. Data sharing is, of course, more than just dumping your raw data in a repository - to be useful, the data require annotation, even if that is little more than plain text labels for columns and a glossary of observation codes. So behavior researchers need to up their game to overcome the challenges of slow data accumulation dribbling into a leaky pipeline.
I became interested in ontologies and knowledge representation for behavior because I, rather optimistically, it turned out, thought a flood of behavior data would follow the flood of molecular data. Ontologies have played an important role in making sense of genes and proteins, and are slowly starting to contribute to morphological studies, but behavior and especially behavioral ecology and ethology lag behind even other branches of ecology in making use of ontologies. There is some motion towards an ontology (or sub-ontology) for behavioral ecology, follow me here for updates.
As challenging as the data situation is, I worry that the modeling side is in complete disarray. Models of the evolution of behavior are frequently descriptive and of little use for inference. For example, there is a sizable collection of models for the evolution of sexual signals, but I defy anyone to throw these models on branches of a tree and generate likelihood estimations of the history of signaling in any clade. Note that this isn't the same as applying an Brownian or OU model of change to a particular measurement or set of measurements sampled from a signal and testing for the presence of selection - Brownian motion is not a model of sexual selection and it isn't clear (at least to me) that there is a way to go from a descriptive model of sexual selection to a something that would yield up a likelihood estimate.
If there is work being done here, it is either well ahead of its time or not being recognized for what it is. Please prove me wrong on this. Meanwhile, I can only hope that the time for this theory to model link is not too far off.
Rather than end on such a pessimistic note, I will suggest two places to start looking for temporal depth. These won't solve the model problem, but they may yield up data that could support some development and testing. The first is the fossil traces of behavior - this means both behavior inferred from morphological fossils as well as, secondarily fossil artifacts and trace fossils. I have some reservations about the later, simply because it is frequently hard to identify the organism(s) involved.
The second is the study of cultural change, both human and animal. There are a lot of interesting questions here, especially at the group/population level, though the link to heritable genetic change still has a long ways to go.
I know not everyone in the comparative methods community is going through the stages of grief that Wayne Maddison discussed in his SSB talk. The community response to his questionnaire reflected optimism for new methods, though I don't know how many behaviorists were surveyed. I did speak with Emilia Martins in the ABS meeting a few weeks later and she was more optimistic about the state of comparative methods. I hope she's right and that the behavior community will find a welcome from the comparative methods community when we manage to shake off the fog of our data amnesia.
The main part of the meeting was bracketed by two 'panel' discussions (I scare quote the word panel because the panel was two people in each case). The first panel consisted of David Hillis and Antonis Rokas arguing whether models or data would be more important going forward. Not surprisingly for this meeting, the focus was on molecular methods, particularly genomic comparative analysis. Interesting question, but of course both are viable research paths at this point - gathering and managing rapidly growing data sets and refining the models of molecular evolution to more realistically mimic the actual processes are both worth pursuing.
The question of data vs. models came up several times, including during another panel discussion of putting dates on time trees. This seems to be a very fertile area for developing improved models and statistical methods at the moment, while the corresponding fossil data is accumulating at a steadier pace.
The second panel was Wayne Maddison and Cécile Ané discussing the limits of comparative methods. The issues that Wayne raised are ones I know firsthand, mostly from my stint in his UBC lab. The issue is that most or all comparative methods for discrete trait values suffer from phylogenetic non-independence, despite 25 year-old claims to the contrary. I spent some time thinking about these issues, but the best discussion at this point is the Maddison and FitzJohn (2014; doi:10.1093/sysbio/syu070) paper. The situation is somewhat better for continuous traits, though there are always questions of model adequacy. I'll admit I don't remember a great deal of Ané 's discussion of limits of OU methods, though it seemed someone more optimistic for the continuous trait cases that OU applies to. Wayne did point out that tip data won't help answer the question of trends in evolution - you'll need fossil data for that.
Thinking about the situation after the meeting wrapped up, I was struck about the differences between different trait domains. In molecular biology we have lots of data and a selection of models that are at least plausible representations of things that actually happen (not perfect by any means, but GTR is a reasonable stochastic approximation of what happens at a single site). Lots of data allow a certain freedom to 'run about' the non-independence problems mentioned in the last paragraph - with enough sites, you could, in principle, assume independent changes. Molecular data also provide a small, but real sampling of fossil data and useful amounts of molecular evolution can occur over experimental time-scales. Thus, molecules provide lots of data, a solid starting point for models, and some temporal depth. Morphology has fossils, a reasonable and slowly growing dataset and a mix of continuous and discrete trait models. Are Brownian motion and OU models good stochastic approximations of morphological change for continuous characters? Not necessarily, but they are definitely a start. As noted above, the situation for discrete characters, even using model-based (Likelihood and Bayesian) methods is rather problematic. However, you aren't limited in your ancestral reconstructions to using contemporary data. This won't solve these problems, but they might give you confidence in your analysis. There is room for optimism here, particularly the hope of better models and statistical methods to make the most of the data available, while new data trickle in.
Then we come to behavior: no fossil data and not a lot of data at all relative to molecular traits. Behavior also has the problem of much of the data being transient - if not captured on a recording device, it's just an observer's memory. Apart from the lost opportunities to capture data, the animal behavior community has been slow to embrace the culture of data sharing, as discussed in Caetano and Aisenberg's (2014; http://dx.doi.org/10.1016/j.anbehav.2014.09.025) Forgotten Treasures paper. Data sharing is, of course, more than just dumping your raw data in a repository - to be useful, the data require annotation, even if that is little more than plain text labels for columns and a glossary of observation codes. So behavior researchers need to up their game to overcome the challenges of slow data accumulation dribbling into a leaky pipeline.
I became interested in ontologies and knowledge representation for behavior because I, rather optimistically, it turned out, thought a flood of behavior data would follow the flood of molecular data. Ontologies have played an important role in making sense of genes and proteins, and are slowly starting to contribute to morphological studies, but behavior and especially behavioral ecology and ethology lag behind even other branches of ecology in making use of ontologies. There is some motion towards an ontology (or sub-ontology) for behavioral ecology, follow me here for updates.
As challenging as the data situation is, I worry that the modeling side is in complete disarray. Models of the evolution of behavior are frequently descriptive and of little use for inference. For example, there is a sizable collection of models for the evolution of sexual signals, but I defy anyone to throw these models on branches of a tree and generate likelihood estimations of the history of signaling in any clade. Note that this isn't the same as applying an Brownian or OU model of change to a particular measurement or set of measurements sampled from a signal and testing for the presence of selection - Brownian motion is not a model of sexual selection and it isn't clear (at least to me) that there is a way to go from a descriptive model of sexual selection to a something that would yield up a likelihood estimate.
If there is work being done here, it is either well ahead of its time or not being recognized for what it is. Please prove me wrong on this. Meanwhile, I can only hope that the time for this theory to model link is not too far off.
Rather than end on such a pessimistic note, I will suggest two places to start looking for temporal depth. These won't solve the model problem, but they may yield up data that could support some development and testing. The first is the fossil traces of behavior - this means both behavior inferred from morphological fossils as well as, secondarily fossil artifacts and trace fossils. I have some reservations about the later, simply because it is frequently hard to identify the organism(s) involved.
The second is the study of cultural change, both human and animal. There are a lot of interesting questions here, especially at the group/population level, though the link to heritable genetic change still has a long ways to go.
I know not everyone in the comparative methods community is going through the stages of grief that Wayne Maddison discussed in his SSB talk. The community response to his questionnaire reflected optimism for new methods, though I don't know how many behaviorists were surveyed. I did speak with Emilia Martins in the ABS meeting a few weeks later and she was more optimistic about the state of comparative methods. I hope she's right and that the behavior community will find a welcome from the comparative methods community when we manage to shake off the fog of our data amnesia.
Labels:
Behavior,
Comparative Method,
Evolution,
Meetings,
Ontologies
Saturday, August 17, 2013
ABS 2013 Wrap up
It's been two weeks since ABS 2013 finished up. So, definitely need to get the rest of these out before I forget.
The theme of why so few comparative studies continued to pop in talks, from a brief mention in Patricia Gowaty's Tuesday morning plenary talk, to Daniel Caetano's plea for more data sharing, ironically comparing the data sharing situation to that in genomics and indirectly in phylogenetics - where the deposit situation isn't as rosy as in genomics, though certainly better than in behavior (shout out to Terry Ord and his growing collection of Dryad deposits). One interesting comparative talk by Odom reconstructed that female song was present in the ancestry of songbirds, a conclusion that was dependent inclusion of a representative sample of taxa outside the northern temperate zone.
I missed a fair number of talks due to ongoing commitments, but managed to catch a number related to spiders, cognition, and a couple of the social learning talks on the final contributed session. One of my favorite spider talks was Elizabeth Jakob's look at visual perception in jumping spiders - in particular a study of biological motion which used moving dot animations constructed by an undergraduate. I spent some time looking at biological motion perception in pigeons a long time ago, so to see that jumping spiders can distinguish spider-like animations from scrambled dot animations was quite amusing. Another spider talk that caught my attention was Schwartz's Allee talk on spontaneous male death in the Dark Fishing Spider. Although this work was published a few weeks before, the talk filled in a lot of details I missed in the paper. Overall spiders were well represented, including Andrade's plenary talk on spider sociality.
There were also some good (and not so good) presentations in cognition and social learning. A nice comparative study across 9 families of mammalian carnivora showed widespread (8 of 9 families, excluding Herpestidae) ability to solve a box opening task involving a latch (though not every species in the 8 families could solve the task). The question being asked was whether sociality (as measured by group size) was predictive on performance in the task - it wasn't. What did predict task performance was the size of the repertoire of actions used to manipulate the box and neophobia (negatively). There was also a suggestion that brain size was predictive. I'm very cautious about that last result - there have been too many poorly done brain size studies and this analysis seemed to be an after thought. I saw a couple of cephalopod cognition talks that I didn't find convincing - I know cephalopods, especially free living, are hard to study, but that's all the more reason to throughly understand the issues involved before spending hundreds of hours of data that fail to address all the alternative explanations.
There were a number of good social learning talks on the last day - I unfortunately missed a good one on social learning in Drosophila, but did see Simon Reader's talk on conditions that influence choices of learning strategy, using guppies, which have become another good model system for social learning. Ipek Kulahci looked at the role of social networks (both positive and negative relations) on demonstrator effectiveness in two Corvus species (C. corax and C. corone). She looked at the effect of relationship on both attention to the demonstrator (observers were free to ignore demonstrators completing a box task designed to minimize scrounging) as well as learning effectiveness.
Apart from the talks, this was a good meeting for socializing - being the 50th anniversary meeting of the ABS, lots senior and emeritus people were there, including my advisor Jack Hailman. There was also more focused socializing, especially as several us continued our planning for next year's followups for the Behavior Ontologies workshop from last February.
The theme of why so few comparative studies continued to pop in talks, from a brief mention in Patricia Gowaty's Tuesday morning plenary talk, to Daniel Caetano's plea for more data sharing, ironically comparing the data sharing situation to that in genomics and indirectly in phylogenetics - where the deposit situation isn't as rosy as in genomics, though certainly better than in behavior (shout out to Terry Ord and his growing collection of Dryad deposits). One interesting comparative talk by Odom reconstructed that female song was present in the ancestry of songbirds, a conclusion that was dependent inclusion of a representative sample of taxa outside the northern temperate zone.
I missed a fair number of talks due to ongoing commitments, but managed to catch a number related to spiders, cognition, and a couple of the social learning talks on the final contributed session. One of my favorite spider talks was Elizabeth Jakob's look at visual perception in jumping spiders - in particular a study of biological motion which used moving dot animations constructed by an undergraduate. I spent some time looking at biological motion perception in pigeons a long time ago, so to see that jumping spiders can distinguish spider-like animations from scrambled dot animations was quite amusing. Another spider talk that caught my attention was Schwartz's Allee talk on spontaneous male death in the Dark Fishing Spider. Although this work was published a few weeks before, the talk filled in a lot of details I missed in the paper. Overall spiders were well represented, including Andrade's plenary talk on spider sociality.
There were also some good (and not so good) presentations in cognition and social learning. A nice comparative study across 9 families of mammalian carnivora showed widespread (8 of 9 families, excluding Herpestidae) ability to solve a box opening task involving a latch (though not every species in the 8 families could solve the task). The question being asked was whether sociality (as measured by group size) was predictive on performance in the task - it wasn't. What did predict task performance was the size of the repertoire of actions used to manipulate the box and neophobia (negatively). There was also a suggestion that brain size was predictive. I'm very cautious about that last result - there have been too many poorly done brain size studies and this analysis seemed to be an after thought. I saw a couple of cephalopod cognition talks that I didn't find convincing - I know cephalopods, especially free living, are hard to study, but that's all the more reason to throughly understand the issues involved before spending hundreds of hours of data that fail to address all the alternative explanations.
There were a number of good social learning talks on the last day - I unfortunately missed a good one on social learning in Drosophila, but did see Simon Reader's talk on conditions that influence choices of learning strategy, using guppies, which have become another good model system for social learning. Ipek Kulahci looked at the role of social networks (both positive and negative relations) on demonstrator effectiveness in two Corvus species (C. corax and C. corone). She looked at the effect of relationship on both attention to the demonstrator (observers were free to ignore demonstrators completing a box task designed to minimize scrounging) as well as learning effectiveness.
Apart from the talks, this was a good meeting for socializing - being the 50th anniversary meeting of the ABS, lots senior and emeritus people were there, including my advisor Jack Hailman. There was also more focused socializing, especially as several us continued our planning for next year's followups for the Behavior Ontologies workshop from last February.
Tuesday, July 30, 2013
ABS 2013 Part 1
It's been a productive, though at times frustrating, first 24 hours at the 2013 Animal Behavior Society meeting. I met last night with one of my long time behavior ontology collaborators. We are planning two NBO focussed events next year. The second one will definitely be during the break between ISBE and ABS next summer. The first, which will be more technically focussed will likely be around the time of the next Phenotype RCN summit though it might be at a different time or venue.
Before I arrived yesterday, they held a public outreach day and apparently the human habituated wolves they brought onto the U Colorado campus were a big hit. Continuing the canine theme this morning, the plenary was on 'Why we love dogs' - discussing various behaviors dogs and their owners use to maintain their bonds. After the Plenary and coffee (sort of, only decaf was left by the time I got through the line), I spent most of the morning in the predation session. The primary talks of interest to me was one on ontogeny of newly hatched spiderlings, and one on resource patch decision making by slime molds. The spider study (on a central american Pholcid species it turns out) demonstrated that the newly hatched spiderlings could respond appropriately with differing levels of attack intensity to differing prey (Drosophila vs. a local ant species), and that this flexibility was not the result of learning from previous experience (Escalante). The slime mold talk (Reid) mentioned previous work that showed slime mold could find the minimum distance through a maze between two food sources through a type of 'distributed processing.' Another talk of interest described a study of chunking and the limits of memory used by caching squirrels (Jacobs). The ABS tweeters have settled on #2013ABS as several other groups have been using ABS2013.
My favorite tweet of the morning was certainly this one:
Before I arrived yesterday, they held a public outreach day and apparently the human habituated wolves they brought onto the U Colorado campus were a big hit. Continuing the canine theme this morning, the plenary was on 'Why we love dogs' - discussing various behaviors dogs and their owners use to maintain their bonds. After the Plenary and coffee (sort of, only decaf was left by the time I got through the line), I spent most of the morning in the predation session. The primary talks of interest to me was one on ontogeny of newly hatched spiderlings, and one on resource patch decision making by slime molds. The spider study (on a central american Pholcid species it turns out) demonstrated that the newly hatched spiderlings could respond appropriately with differing levels of attack intensity to differing prey (Drosophila vs. a local ant species), and that this flexibility was not the result of learning from previous experience (Escalante). The slime mold talk (Reid) mentioned previous work that showed slime mold could find the minimum distance through a maze between two food sources through a type of 'distributed processing.' Another talk of interest described a study of chunking and the limits of memory used by caching squirrels (Jacobs). The ABS tweeters have settled on #2013ABS as several other groups have been using ABS2013.
My favorite tweet of the morning was certainly this one:
Animal behavior studies are rarely comparative. Need to gather data, store and make it available. Phylogenies are needed too! #2013ABSThe phylogenies have gotten better and more comprehensive, but the gathering and sharing of comparative data still has a long way to go.
— Daniel Caetano (@darkymoss) July 29, 2013
Tuesday, July 23, 2013
AAS 2013
Here's a belated report from the 2013 American Arachnological Society meeting last week. While I was there I tweeted a couple of times and @nsandlin tweeted about nearly all the talks. Time to get this off my plate before Animal Behavior next week.
I found several talks quite memorable, including Eileen Hebets talk that seems to represent a start at integrating all the multi-modal signaling data for Schizocosa she's accumulated over the past 15-20 years. I also liked Igni Agnarsson's talk on the diversity of Malagasy Anelosimus - lots of related species in close proximity, and unlike their North American sister clade, all remain sub-social.
Another memorable talk, if for more personal reasons, was Angela DiDomenico's (student of Marshal Hedin) systematic work with the Opilione genus Sitalcina. Turns out there is likely an undescribed species in a draw only a couple of miles from where I attended Junior High School in Palos Verdes. I'm not really surprised - the ecology of Palos Verdes has been known to include endemics for a while now (remember the Palos Verdes Blue butterfly?). Hopefully this (not so traditionally charismatic) arachnid will have a better future than the PV Blue butterfly.
I knew that George Uetz had done a lot with the Schizocosa system, but the shear number of Schizocosa talks, especially during the second Monday morning session, was a bit of a shock. S. ocreata really is attaining model organism status.
Apart from the talks, I got to catch up with people I knew in the Tucson Maddison lab, particularly Greta Binford, who indicated that several spider genomes are either done or nearing completion. Having the genome sequenced is not the same as the level of annotation we have in vertebrate model organisms, but it is a step towards the day we could do a Phenoscape like project for spiders.
I also briefly chatted with Eileen and with Jonathan Coddington, who I got to know a bit from some phenotype ontology activities prior to the launch of the RCN.
The meeting also offered several opportunities to add to my literature collection, and I took advantage of the honor system reprint table as well as a couple of items in the silent auction.
I found several talks quite memorable, including Eileen Hebets talk that seems to represent a start at integrating all the multi-modal signaling data for Schizocosa she's accumulated over the past 15-20 years. I also liked Igni Agnarsson's talk on the diversity of Malagasy Anelosimus - lots of related species in close proximity, and unlike their North American sister clade, all remain sub-social.
Another memorable talk, if for more personal reasons, was Angela DiDomenico's (student of Marshal Hedin) systematic work with the Opilione genus Sitalcina. Turns out there is likely an undescribed species in a draw only a couple of miles from where I attended Junior High School in Palos Verdes. I'm not really surprised - the ecology of Palos Verdes has been known to include endemics for a while now (remember the Palos Verdes Blue butterfly?). Hopefully this (not so traditionally charismatic) arachnid will have a better future than the PV Blue butterfly.
I knew that George Uetz had done a lot with the Schizocosa system, but the shear number of Schizocosa talks, especially during the second Monday morning session, was a bit of a shock. S. ocreata really is attaining model organism status.
Apart from the talks, I got to catch up with people I knew in the Tucson Maddison lab, particularly Greta Binford, who indicated that several spider genomes are either done or nearing completion. Having the genome sequenced is not the same as the level of annotation we have in vertebrate model organisms, but it is a step towards the day we could do a Phenoscape like project for spiders.
I also briefly chatted with Eileen and with Jonathan Coddington, who I got to know a bit from some phenotype ontology activities prior to the launch of the RCN.
The meeting also offered several opportunities to add to my literature collection, and I took advantage of the honor system reprint table as well as a couple of items in the silent auction.
Sunday, April 21, 2013
This summer
After going to Evolution and iEvoBio for the past three years, it's time for a change. I'll be heading back to the Animal Behavior Society meeting this summer (representing myself this time), and, for the first time in 11 years, I'll be attending the American Arachnological Society meeting. I'm not turning my back on Evolution or the interesting community developing in Evolutionary Informatics - I expect to be back in the Triangle for the Evolution Meetings next year.
Meanwhile, I'll hope to have some interesting reports, both here and on twitter (@pmidford) and looking forward to meeting old and new friends.
Meanwhile, I'll hope to have some interesting reports, both here and on twitter (@pmidford) and looking forward to meeting old and new friends.
Monday, June 11, 2012
ABS 2012 - It's different this time
I've finally made it back to full attend an ABS meeting for the first time in five years (I last presented at the 2007ABS in Vermont). I'm here in a different role this time though, not as a postdoc or an ontology contractor. I'm attending talks for the first couple of days, then representing the Dryad repository at an exhibitor's table, which will extend into the first days of the following HBES meeting.
I haven't stopped doing ontologies or thinking about spider behavior (I caught talks on Black Widow sibling cannibalism and jumping spider vision this morning - the later talk included some courtship clips that looked very familiar). And although I've stopped work on OWLWatcher, I have a more focussed project related to spider behavior and one more in keeping with NESCent's focus on synthesis. More about that later.
For the moment, I will spend the time catching up with behavior people, making new contacts, and enjoying some talks. You can catch me on twitter at @pmidford, or follow the tag #abshbes2012.
I haven't stopped doing ontologies or thinking about spider behavior (I caught talks on Black Widow sibling cannibalism and jumping spider vision this morning - the later talk included some courtship clips that looked very familiar). And although I've stopped work on OWLWatcher, I have a more focussed project related to spider behavior and one more in keeping with NESCent's focus on synthesis. More about that later.
For the moment, I will spend the time catching up with behavior people, making new contacts, and enjoying some talks. You can catch me on twitter at @pmidford, or follow the tag #abshbes2012.
Thursday, May 28, 2009
This summer
I'll be attending two meetings this summer: Evolution 2009 (Moscow ID) 12-16 June and ICBO (International Conference on Biomedical Ontologies - Buffalo NY) 24-26 July. I'll be presenting some of my recent work with BiSSE at the Evolution meeting (my first non-ontology talk for a while) and representing Phenoscape at ICBO with a poster. Of course the rest of Phenoscape will be at ASIH in Portland while I'm in Buffalo, but it made sense to have Phenoscape represented both places. I'll miss Portland, but Evolution is there next year.
I'm mentoring another Google summer of code project - my student will be developing a Mesquite package that will read and display Phenex annotations to character matrices. Getting Phenex to talk to Mesquite is an important, relatively low-hanging fruit for Nexml to enable, and just the sort of thing I've been trying to do with Nexml for a while now.
I will be leaving Kansas at the end of August and headed (indirectly) to NESCent to start an ontology alignment project. I'm hoping to develop something that might be useful as a prototype both to Phenoscape as well as a core component to EthoOntos, the comparative method backend to OwlWatcher.
I'm mentoring another Google summer of code project - my student will be developing a Mesquite package that will read and display Phenex annotations to character matrices. Getting Phenex to talk to Mesquite is an important, relatively low-hanging fruit for Nexml to enable, and just the sort of thing I've been trying to do with Nexml for a while now.
I will be leaving Kansas at the end of August and headed (indirectly) to NESCent to start an ontology alignment project. I'm hoping to develop something that might be useful as a prototype both to Phenoscape as well as a core component to EthoOntos, the comparative method backend to OwlWatcher.
Sunday, June 15, 2008
Getting ready for Minneapolis
The evolution meetings in Minneapolis start late this week. For me the meeting will start on Friday, with the Ontology workshop. I'll be giving a 20 minute talk on taxonomy ontologies. The workshop has been booked full for several months now. I am also associated with three posters: one from a comparative methods in R workshop I attended last December, another one from Phenoscape, which gives an update on the TTO, TAO and where we are headed with Phenote and the new workflow, and finally my single author poster on the behavior work. Part of this will be explaining the difference between annotating publications and behavior videos, and part will be an update, not so much on OwlWatcher, but a preliminary discussion of a toy implementation of the EthOntos-Lite alignment module. There is, as of today, running code, but I haven't given it anything more an a couple of trivial examples, which it seems to handle correctly. It would have been nice to have something I could feed OwlWatcher projects into, but that will have to wait - I've still got lots on my plate, despite a productive weekend.
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