Gaurav Vaidya

Welcome to my blog!

Hi there, and thanks for stopping by! If you'd like to know more about me, see my curriculum vitae, read about software I've worked on, or just head straight for my Twitter feed. There's many ways of contacting me if necessary. Cheers!

Ricardo Reis and me

People who know me know that, even as I acknowledge Lolita as the finest novel I've ever read, my heart belongs to my favouritest novel in all the world, the little known The Year of the Death of Ricardo Reis, a novel published in 1984 by genius Portuguese novelist José Saramago, who died last June at the age of 87. Saramago wrote Year of the Death when he was 62, and death is very much at the heart of the novel. But that's not why I like it.

On the surface, Year is an almost unbelievably dull book. Spoilers begin: Reis, a nobody Doctor who has lived in Brazil for years, has migrated back to Lisbon after learning of the death of his friend Fernando Pessoa. He spends a listless year falling in love with the young, unobtainable Marcenda, who in her shy way responds to his affection; while sleeping with Lydia, the chambermaid at his hotel, an affair he hides from the world. The ghost of Fernando Pessoa meets him occasionally, bringing wisdom, humor and friendship from a afterlife shrouded in darkness. Twisty plotlines following the state's suspicion of his sudden return to Portugal, the power dynamics at the hotel at which he stays, and his delicate balancing of his two, different loves. And then, on the second last page of the novel, as its title promises, Pessoa's ghost arrives to usher Reis into the afterlife.

So, why the love? I always knew that it was because I felt a link with Reis, buffeted by the forces of love, desire, boredom, fear and society, and unable to do more than to batten down his hatches, to take joy in a cold, friendless life when and where he could. Reis is a man who slips so quietly and unceremoniously out of his own life that nobody except the grieving Lydia and her unborn child -- Reis' only legacy -- notice his passing.

Tonight, I compare my behavior in areas like science and Wikipedia -- where I believe I would push to have my way, in some shape and form, if I was convinced that truth was on my side -- with how I act and react to human relationships. The twisty thing about simultaneously feeling worthless and unique is that you never, ever want to stand up for yourself. It's the path in the middle: the worthless part of my psyche insists that imposing myself on another human being is a crime, right up there with talking loudly on a phone on a bus, while the egotist in me insists that, welp, hey, if they don't want to interact with me, it's their own loss.

No, it isn't. And this is important.

Another teeny, tiny little point: there is one, single bit in the entire book where Reis goes out and does something. Knowing that Marcenda is heading to Lourdes in a final attempt to heal her paralyzed arm, Reis heads there himself to plead his case, to risk all in the name of love blah blah and so on and so forth. But, this final foray into standing up for his own affection, to condemn with his actions the line fate has drawn for him, is an utter failure. The lesson learned is not to fight.

Post scriptum (Dec 19, 2011): Bob Corbett reminds me of these glorious lines from the novel:

... human unrest is futile, the gods are wise and indifferent, and above them is fate, the supreme order to which even gods are subject. And what of men, what is their function. To challenge order, to change fate. For the better. For better or for worse, it makes no difference, the point is to keep fate from being fate.

So.

Blogging elsewhere, because I can

While I have been letting this blog fall asleep in the run-up to the ever-so-busy final weeks of school, I have been busily blogging, writing and scheming elsewhere! Here are some updates:

October 11

Co-wrote What’s new, October edition on the Map of Life blog.

November 18

Kicked off a WikiMedia Commons project for the Biodiversity Heritage Library. So far, we've tagged 16 files from BHL, fixing their copyright status and linking back to the BHL website in the process. Jean-Frédéric created this gorgeous template to use as a source template on BHL images. The plan (my plan) is to keep tagging images into the New Year, and see where we are after that.

November 29

Kicked off a project with Robert Guralnick and Andrea Thomer, working closely with the CU Museum of Natural History and with help from the NSIDC (don't you love big-team projects?), to digitize the field notebooks of Junius Henderson, the CU Museum's first curator. We were all surprised at how amazing WikiSource is for managing transcriptions and displaying the results.

December 5

Co-wrote Field Note Challenge Part 2: Veni, Vidi, Wiki on the So You Think You Can Digitize blog.

December 6

Excited by all the taxonomically interesting information already in WikiSource, I created a portal to try to coordinate efforts to annotate, organize and connect these resources with counterparts on WikiSpecies, Wikipedia and (especially) the WikiMedia Commons.

Fun times! I brazenly anticipate even. more. fun as I get a week to push ahead on the Map of Life after Tuesday, followed by a week of fun with sister and cousins in East Brunswick, NJ, followed by another week to code, ruminate and discuss, followed by another two weeks (back in Boulder, now) to work on things before the next semester smashed into my life like a grammarian smashing into someone misusing a simile.

Remembrance Day 2011

We who are left how shall we look again
 Happily on the sun or feel the rain
 Without remembering how they who went
 Ungrudgingly and spent
Their lives for us loved, too, the sun and rain?

-- Wilfrid Wilson Gibson, Lament (1916)

(I have others)

TDWG 2011, day two, part two: Global biodiversity informatics initiatives update

My post on TDWG 2011, day two, part two, starts at 2pm with the symposium on "Global biodiversity informatics initiatives update". This symposium was hugely useful to me as a biodiversity noob, giving me a broad overview of the major #biodinfo initiatives, which problems they are tackling, and where they are headed. I don't need to repeat that these are all based on my very wonky notes; all errors here are mine, and -- when you spot them -- please let me know in the comments section. The talks in this symposium were:

• Eamonn O'Tuama talking about the Global Biodiversity Information Facility (GBIF) and its recent improvements, including:

  Switching to using DarwinCore Archives as an input format: spreadsheets are easier for people to work with than XML! It now takes a month for new data to go from upload to being published; GBIF's goal is to get that down to a week.

  GBIF has also revamped their taxonomic validation, adding other authority checklists their current taxonomic authority, the Catalogue of Life. In fact, they're now assembling a database of taxonomic checklists! I wonder if they'll show the changes in checklists over time.

  A brand new GBIF Online Resource Center has been set up to make it easier for people to find out about and upload data to GBIF.

  There are some really exciting projects which could potentially use GBIF data and TDWG standards: the Wallace Initiative, the ICLEI and the IAIA.

• William Ulate talked about the Biodiversity Heritage Library, with a presentation explaining how the BHL network looks today, with nodes spread out across the planet. Books, journals and periodicals are uploaded through BHL nodes, and are then distributed to the others (and to the Internet Archive). Prime among these were BHL Europe and BHL-Australia (a part of the Atlas of Living Australia); he particularly noted BHL-Au's fantastic user interface, which will form the basis of UI improvements to the US website. He also mentioned BHL's Egyptian collaborator, Bibliotheca Alexandrina (a project older than BHL itself!).

  William also pointed out that anybody could suggest books or journals for BHL to scan, and they would try their best to do it as fast as possible. Also, BHL's source code -- including the code that powers their website, APIs, and Citebank -- is publicly available.

  BHL is also developing CiteBank, a database of biodiversity citations. Put that together with Rod Page's iTaxon idea, and you can see some really amazing -- and amazingly useful! -- interlinks between taxonomic names and literature happening.

• The Taxonomic Name Resolution Service was mentioned. It is a really cool project to standardize plant taxonomic names. And yes, an API is available!

• Cyndy Parr presented on updates from the Encyclopedia of Life (EOL) project. She pointed out that EOL is all about aggregating and curating data; it's never going to be as smooth as Wikipedia, where all the data is in one place. However, it can have better import processes: all new names on ZooKeys/PhytoKeys are immediately added to EOL; it can also get feedback and corrections back to the original publishers much more efficiently than Wikipedia can.

  Cyndy also showed off EOL collections of taxa, across any kingdom of life and collected by any criteria, from birds at the Smithsonian's National Zoo to the colour blue. Collections can have EOL communities form around them.

  Another exciting development: EOL is going multilingual, with a little help from TranslateWiki. And they're planning collaborations with iNaturalist, one of the best websites for naturalists I know.

  EOL also plans on moving to DarwinCore Archives flat-files, as an easier way of moving data in and out of their system. They have released a the largest possible phylogenetically-organized tree, representing the state of our phylogenetic knowledge.

• Donald Hobern spoke about developments at the Atlas of Living Australia (ALAu) focusing -- much to my excitement -- on taxonomic issues.

  He began by talking about descriptive taxonomy. He mentioned IdentifyLife, a database of identification keys, including -- get this -- a plan to build a single, gigantic Key to All Life. The idea is to support citizen science "in the broadest sense". ALAu is working on a project to port the DEscriptive Language for TAxonomy (DELTA) software suite into Java. Finally, he mentioned the Taxonomy Research and Information Network (TRIN), which hosts a pretty well-organized wiki.

  Donald pointed out that ALAu's taxonomy arm had two primary communities to serve: the one interested primarily in geographical data, and the one interested primarily in taxonomic/collection data. I think he demonstrated this division by comparing the Australian National Herbarium datasets with Australia's Virtual Herbarium, but to be honest, my notes are somewhat in disarray at this point. This is because Donald is an excellent presenter, and so I wasn't focusing on my notes so much. Sorry about that!

• The symposium ended with Dave Roberts talking about ViBRANT. He spoke mainly about the exciting new changes coming in Scratchpads 2.0, which -- based on Drupal 7 -- will have a prettier user interface, snappier access times, and much better scalability. There are ambitious plans to plug in Scratchpads to biodiversity publishers (such as PenSoft) as well as biodiversity producers and consumers (such as the Encyclopedia of Life and LifeDesks). Even more interestingly, they're setting up a job-processing backend for Scratchpads on the Oxford Batch Operations Engine (OBOE).

  A sandbox Scratchpad is available, if you want to play around with the technology in its current state. Their source code is available, including Scratchpads 2.0. And, being on Git, all that code is easy to play with.

TDWG 2011, day two, part one

After a short trip to meet Walter Jetz at Yale, I'm back in Boulder, have seen Paul Simon in Broomfield, CO and Wikipedia Loves Libraries! at Norlin last week, and am making a start at putting together my research ideas. Fun times ahoy!

But first, I'm still working through my notes from TDWG 2011. Here's a first installment of my treasure trove from day two; obviously, many awesome presentations and parallel talks were missed, probably because I was too busy enjoying them to take down notes. All errors are mine, and when you spot them, please do let me know in the comments!

• Islandora (p. aye-lan-do-ra) is a slick, open-source digital asset management system based on the popular Drupal CMS. Islandora was developed by the University of Prince Edward Island's Robertson Library. Islandora's goal is to steward digital assets in the long term, with an emphasis on long term stability, and to manage the entire research life cycle. Interestingly, the developers of Islandora provide paid support for their software through a private company, DiscoveryGarden, which I can think can be a valuable way of supporting scientific software development and maintenance. The presentation and demo (which I unfortunately missed, because of parallel sessions) was given by Mark Leggott, Islandora's Lead.
• If you want to play around with Islandora, their Sandbox instance is automatically reset regularly.
• The Field Book Project at the Smithsonian aims "to create one online location for scholars and others to visit when searching for field books and other field research materials". Sounds interesting! Unfortunately, I missed their presentation at TDWG; I'm hoping the So You Think You Can Digitize blog will cover them soon.
• FishNet 2 has a pretty slick interface, allowing search by a number of common fields or by drawing polygons on a map. Search results allow taxonomic checklists to be quickly assembled and downloaded as a CSV, among other features. You can definitely see the basis for a really fantastic data exploration tool here, and - being part of VertNet - definitely opens the possibility of a really first-rate data exploration tool for all those vertebrate records. And yes, there's an API as well. A good idea: FishNet 2 saves all search queries, so that developers can analyze what users are looking for.
• Aaron Steele and John Wieczorek demoed the Darwin Core Engine, the heart of VertNet. The plan is to create an application on Apache CouchDB, a "document-oriented database that can be queried and indexed in a MapReduce fashion using JavaScript", using the magic of HTML5 as the controller to CouchDB's model. The end result: speed, maintainability, scalability. I'm definitely looking forward to more about that. And - I only just noticed they - they credited "Dennis Ritchie for C and Unix, Steve Jobs for our Macs". Aww.
• If you want to play around with this, try IRIS Couch, a CouchDB hosting service.
• Adrian Thomas Hine at the NHM Department of Entomology had an interesting talk on Species-level Metadata collection in museum; his argument in a nutshell being that even assembling species-level (rather than specimen-level data) could be valuable for research. He argued that this was also more sustainable, since maintaining this species-level index was a daily job for curators, and would answer a key question: what does a museum actually have?
• Cam Webb is working on modeling botanical data for the semantic web, based on DarwinCore.
• Filtered Push is a way to push annotations around between online repositories. My understanding of this tool is: if an analysis tool finds a specimen entry from GBIF suspicious, the dream is to allow the tool to "push" an annotation to GBIF, which GBIF can in turn "push" to the distributing museum for examination and verification by a curator. In this way, data can be improved across the interconnected databases we are now building.
• Ontobrowser, an "interactive ontology navigator and ontology-based image retrieval system", is a pretty good way of navigating Morphster, a "demonstration prototype of a service-oriented architecture enabling and supporting morphologically based phylogenetic studies". Try it out on the Hymenoptera!
• Chris Freeland talked about BHL's new Darwin Library Collection, "a digital edition and virtual reconstruction of the surviving books owned by Charles Darwin". They used detailed notes from di Gregorio and Gill, Charles Darwin's marginalia vol. 1 to map Darwin's own comments in his own hand onto books already scanned for the BHL, or - in some cases - Darwin's own annotated copies scanned directly into the BHL. Chris gave us a fantastic example of the latter, where Darwin wryly commented on Charles Lyell's thoughts on intraspecific variation that "if this were true, adios theory".
• Donald Hobern talked about annotation and ALAu. There were a lot of useful technical details about ALAu's implementation of annotations, but there are also some really interesting side projects being developed. The Online Zoological Collections of Australian Museums is a collection of animal data from museum across Australia, using the TAPIR protocol to aggregate the data from museum repositories. Identify Life, meanwhile, is a database of identification keys. Their Key to All Life project hopes to build one single gigantic identification key - for everything. How awesome is that? Give it a whirl yourself!
• Bob Morris introduced the Annotation Ontology, and stressed the importance of linking to the proof of what you're saying.

Part two will be out as soon as I can get around to it. Also: getting more and more excited for Life and Literature, just a week away tomorrow. It'll be great to see familiar faces from TDWG so soon after TDWG 2011 New Orleans!

The #SciFund Challenge

I just discovered the #SciFund challenge, a Kickstarter-like project to raise money for scientific projects by promising deliverables created as part of the project. I think it's a great way of getting non-scientists involved in science, to say nothing of getting funded and of creating a concrete science-to-public deliverable system. So: excited!

Here's some of the projects I took a fancy to. Unfortunately for me, as a grad student lacking money, RocketHub (the hosting website) has no mechanism for "subscribing" to a project without paying that I can find. So this might be the only way for me to keep an eye on them (and maybe make a contribution with my next paycheck).

• Collecting ants living nears homes and schools, which sounds like an awesome way to get kids involved in science.
• Genetic surveys of Costa Rican birds and bats, the American pika, and the social tuco-tuco. Because Ctenomys is to love me.
• Hiring local field assistants for elephant research in Sri Lanka, building closer links between researchers and the human residents of the landscapes they study.
• Using Ancient Rome-era DNA to determine the geographical origins of immigrants to the Empire.
• An infrastructure project to deliver vaccines to remote areas by matching up travelers in rural Tanzania with vaccines which need to be delivered to particular villages. That's a really smart idea!
• Do camera traps affect the behavior of their study animals?
• Why do some spinner dolphins have "reversed" fins, which is a fascinating study, mixing up biophysics and evolution/selection pressure research in sexy, sexy ways.
• Tracking dolphin populations through photoidentification, whose project description reminds me that labradors can track killer whales. Which is an awesome thing to be reminded of.
• Parasitic trematodes which change the behavior of the Californian killifish so they get eaten by birds (where the trematode can finish its life cycle).
• Evolution between sunflowers and bees in agricultural fields.
• Explosive duck penis erections, which really needs no elaboration.

The most fascinating part of this enterprise for me is the connection between the science projects and the contributors: the deliverables. Rewards for donating ranged from credit (on websites or in publications), to a copy of the research results, to exclusive access to project blog and Twitter feeds (which make no sense to me: wouldn't you want those feeds to be as public as possible, to encourage more people to join in and contribute?). More interesting deliverables were also on offer, from elephant dung paper and calendars with photos of the research subject, to photos taken during the study, clay sculptures of dolphin fins, lyrics to a Tanzanian children's song, and comics personally drawn for you by Zach Weinersmith of Saturday Morning Breakfast Cereal fame. Allegedly, a comic of "Carl Sagan riding a unicorn" is not out of the question.

One thing I did find odd was the lack of links in the project descriptions. Only a few projects linked to websites, blogs, Facebook pages or Twitter feeds (one project going so far as making the Twitter and blog feeds "contributor only"), although just about all of them had really excellent websites hidden away in the "About Me" section. I love Twitter for letting me follow a project without getting too involved, so more Twitter feeds would have been great to see.

Thinking in the longer term, I wonder how well this would work without the #SciFund banner, though. Unlike music or movie crowdfunding, where artists can put up samples beforehand, it might be harder to prove your scientific worth to a broader audience. For instance, how would I differentiate between a serious project to study bee evolution and some nutjob trying to prove that evolution didn't happen? I could look at the project description, sure, but it's not hard to reference many scientific studies to give yourself an air of authenticity. Perhaps the #SciFund banner will eventually be replaced with institutional banners: if the research is being carried out by the Smithsonian, the University of Colorado or is partially sponsored by National Geographic, you can be pretty sure it's been vetted.

TDWG 2011, day one

Yesterday (Monday) was the first full day at TDWG 2011. This post is an extraordinarily incomplete summary of some of the things I learned that day; a lot happened on that day, and I really don't have time to write about it all here (although I might post my thoughts in future posts). I'm writing down some URLs for my own interest. If I missed something you found interesting, it's likely that I was just too fascinated by the presentation to take notes (see my single sentence describing Michael Donoghue's keynote speech for a perfect example). All errors are mine, and when you spot them, please do let me know in the comments!

• Hank Bart announced the Tulane University Biodiversity Research Institute.
• TDWG Annual Conference 2012 will be at Beijing, People's Republic of China!
• Since 1988, TDWG has been a part of the International Union of Biological Sciences (IUBS), a 92-year old biological organization which inexplicably has scrolling text on its homepage.
• Everybody working at TDWG is a volunteer - including everybody working hard to make TDWG 2011 a success. That's crazy!
• Nozomi James Ytow is the representative for Asia on the TDWG Executive.
• Since 1935, the Index Herbariorum has maintained a list of herbaria around the world. But it does not have a Wikipedia page (as of Oct 19, 2011, anyway). Interestingly, this database has been set up in KE EMu, the popular collections management system, which is also missing a Wikipedia page.
• Audubon Core is "a set of vocabularies designed to represent metadata for biodiversity multimedia resources and collections". Its specification, interestingly enough, is based on a wiki "developing a range of new, much easier and paper-free identification tools, for use within schools and universities across Europe". Interactive/digital keys have come up before, and will come up again, in this conference.
• One good way of helping support TDWG is by collaborating with them on a grant proposal. Who better to work with on biodiversity standards?
• Michael Donoghue had an excellent keynote address to start the conference with.
• So far, 39 awards have been made under the NSF's Advancing Digitization of Biological Collections (ADBC), including InvertNet, and the Consortia of North American Lichens and Bryophytes.
• The TDWG Taxonomic Names and Concepts Interest Group had a meeting, where I found out about a bunch of taxonomic information aggregation and exchange projects around the world. Discussions included:
• A comparison of the Taxon Concept Schema (TCS) and Darwin Core (DwC). If we want to move on to ontologies, the TDWG Ontology came up.
• TDWG's own Global Names Architecture project, which has some exciting things ready already (Global Names Index) and some in the works (GNUB).
• Naim Matasci also mentioned the iPlant Taxonomic Name Resolution Service (TNRS), a pretty utility "for correcting and standardizing plant names". And the source code is available on GitHub, released under a modified BSD license.
• I know how awesome Pensoft Publishers are. But I didn't know about IPNI.
• The BGBM's Biodiversity Informatics Section (BDI) has some fascinating resources available on their website.
• Javier de la Torre showed off the Geospatial Conservation Assessment Tool (GeoCAT). As you would expect from Vizzuality, the website is fast, slick, efficient and easy to understand. And yes, it's on GitHub. Hard to tell if it's open source, though: there ain't no license.
• Denné Reed described a "federated system of data collection" he uses for paleoanthropology. And yes, he uses Darwin Core.

I'm dreading writing tomorrow's blog post, since today (Tuesday) was an incredibly valuable day for finding out about projects, websites, ambitions and niches. Luckily, I don't have to worry about that for a day at least, maybe more.

TDWG 2011, day zero

Here's some fantastic stuff I discovered during the TDWG icebreaker yesterday:

• Mandala, a cross-platform, FileMaker® Pro database "designed to track specimen-based biodiversity data, loans, and detail complex nomenclatural histories with their associated literature". A book chapter describes the schema used, but if you prefer to just jump in and try it out, there is a live database of 130,229 specimens across 2,658 (possibly invalid) taxa citing 952 pieces of literature from the Therevidae (Insecta; Diptera).
  • (Bit of a coincidence there: I co-authored a chapter in the same book! How cool is that?)
• mx, a Ruby-based platform for "gathering and working with data", as per Matt Yoder's blog post explaining his approach to writing software for science, which is a great read if you write any kind of software for any area of science. And mx is available on Github, making it perfect to play around with.
• 3I Interactive Keys and Taxonomic Databases, a "set of software tools for creating on-line identification keys, taxonomic databases, and virtual taxonomic revisions". There are plenty of sample datasets here, too.
• Species File, "both a database and a website: The database provides the detailed information about all taxa contained within the scope of the "apex taxon" and the website provides the means to interact with and modify the information contained in the database", principally developed by David Eades. There are a lot of example 'species file' websites available.

And, off of science, Ray's Site, a blog about a blind cat, and how he navigates a world without his sight.

How awesome is Wikipedia?

Precisely this awesome:

So somebody (probably Wikipedia user midorigin) purchased Milo powder from two countries about two continents apart, photographed them on white paper, added scale lines, and uploaded their result, allowing Wikipedia to visually show the difference between Milo preferences in two very different geographical areas. Think about that one more time: an online, user-contributed, free-to-edit encyclopedia with a serious, well-illustrated discussion of Milo varieties around the world.

Truly, my friends, we are living in the future.

"The stories of the fabulous past"

Thanks to the Letters of Note blog, I just discovered this trove of letters addressed to the children of Troy, Michigan, collected by Marguerite Hart in the early 1970s, who asked dozens of "actors, authors, artists, musicians, playwrights, librarians, and politicians of the day" to pen down their thoughts on this day. I immediately read the letter written by famed actor Vincent Price. I was not disappointed. Here is my transcript of the letter he wrote, a beautiful paean to history, literature, language and libraries.

Dear Young Citizens of Troy,

Many centuries ago in Asia Minor in a city with the same name as yours, literature was born. One of the greatest poets who ever lived sat among his people and told the stories of the fabulous past. And they remembered them down through the years until the legends became fact, the fact not so much of history but of the word, of language.

Your new library is the home of language, yours and all others from the beginning. In it you will learn how others lived and thought and from it you will learn to live and think better for yourselves.

Vincent Price