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Open Source Software & Science Reproducibility

January 14th, 2014

This year my contribution to the AGU fall meeting 2013 was all about the development of Open Source Software to enable the reproducibility of scientific products, with both a Poster and an Oral presentation. The AGU was the perfect opportunity to share my ideas on a topic that is one of my main interests.

This was my 2nd time at AGU, but my first time with an oral presentation which turned in a real challenge!

The main issue was a combination of 2 factors : I had decided to generate the slideshow in realtime as HTML from an online IPython Notebook. I thought it would be cool to show this functionality, as well as the work itself. Unfortunately, I was dependent on an internet connection at the time of the presentation, but alas, at AGU the presenter computer doesn’t have internet connection! Definitely not the best conditions for a web based slideshow generated “on-the-fly” by the execution of an IPython Notebook.

I found out about the lack of connectivity only 2 days before my presentation. I must have misunderstood the AGU oral presentation guidelines, but when I didn’t find an explicit mention of the lack of an internet connection, I took it for granted that that wouldn’t be an issue. Big mistake!

I decided it would be safer to prepare a power-point presentation, and some time later, I had one. Deep breath; I would be safe. But… what a disappointment !

I was so excited about the idea of showing my work running in realtime instead of showing a static (somewhat boring) ppt  presentation!!!

I kept thinking about alternative solutions, though, and an idea quickly came to me. If the lack of internet stands in the way of an interactive, realtime demo there should be no problem in running a static HTML slideshows instead; at least that is what I thought …

I used the IPython “nbconvert” utility and its “convert to slide” option, and I successfully converted my workflow from an interactive IPython notebook running in slideshow mode to a static HTML5 slideshows, yeah! The audience wouldn’t get to see how this was done, but at least they would get to see the result.

Happy with the final HTML presentation I finally went to the “AGU’s Speaker Ready Room” to upload and test my presentation. Unfortunately, my HTML presentation would not run offline. The lack of internet was giving me troubles with missing JavaScript files, missing fonts, images-urls to be replaced with path to static files, broken hyperlinks etc … it was not as easy as I thought.

It took more than 3 hours to fix all the bugs on account of a really slow internet connection running from my phone, but finally i got my presentation perfectly  running off line on the AGU computers !

In the end, my talk ran very smoothly. A complete workflow for “catchments characterization” using exclusively open source software, running online and fully reproducible thanks to the use of open source software and an open dataset! I felt really good, as I think I successfully got my message across, both in words and in actions.

To top it all off, my presentation came just at the right time. Before me, two other presentations during my session had mentioned the use of the IPython Notebook as open source software tool to enable reproducibility of scientific work. They had highlighted that it shows great potential and that it deserves further investigation. I think my presentation gave them even more proof of that! Even the chairman acknowledged this when he stated: “Before we heard about it, but now we saw it in action!” I felt very proud of what I had done. The effort I put into running the HTML slideshow definitely paid off!!!

 

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Three reasons to attend ESIP winter meeting

January 15th, 2013

Erin Robinson has posted 10 reasons to attend the ESIP winter meeting. I want to provide some feed-backs from the point of view of myself.

Interaction: ESIP meetings are different from a normal conference with sessions of presentation and Q/A. Its sessions are more like break-outs and workshops and require interactions from the audience.

Topics: ESIP meetings cover various topics standing in the fore-front of geo-informatics, cyberinfrastructure and semantic web. It is easy to find a session or poster that could be of interest to you.

Location: Normally the ESIP winter meeting will be held at Washington DC. It’s a city full of museums, good food and other interesting stuff. Take a short visit during the meeting time!

I want to share a image which combines a part of my ESIP 2013 winter meeting poster and a photo taken at the National Museum of Natural History (they share a common topic of geologic time scale).

Capture

An additional information is for students in the field of semantics and/or geoinformatics. You may apply the Rob Raskin scholarship.

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Survival and thriving at AGU Fall Meeting 2012

December 11th, 2012

AGU Fall Meeting, if I am correct, is the biggest conference in the field of geosciences. For the year 2012 there were over 22000 people participated in the event. Yet, a conference is more than the number of attendees. AGU is not a single combination of a number of academic meeting sessions. There are various workshops, seminars, town halls, exhibitions and social activities together with it.
I once read an article written by the president of UNISCO (two years ago?), in which it is mentioned that the number of earth scientists across the world is about 440000. This is a tiny number comparing with the global population. While approaching San Francisco and Moscone Center, the city and venue of AGU, I could feel the number of earth scientists around me is increasing sharply. Especially along the 4th street to Moscone Center, what one can see during the AGU week should be called a deluge of earth scientists. Personally, I had an interesting feeling – am I driven by the deluge, or I am a part of it?
Back to the conference itself, it is a big conference so I (1) focused on sessions in the division of Earth and Space Science Informatics (ESSI), and prepared my personal schedule for posters and presentations I was interested. I also set (2) in-person meetings with people with whom we want to discuss some issues related to the research projects DCO-DS and GCIS-IMSAP at TW. There were (3) a number of other workshops and activities together with AGU, such as the workshop of Data Management 101 for Early Career Scientists, the workshop about NSF system, the ESSI reception, the Ignite Talk, etc. Some of them cannot be easily found on the AGU web site, but are informed through different channels. Many thanks to people in those email lists (e.g., AGU-ESSI, ESIP-SW) I joined for sending me the messages.
I gave two presentations on Friday: a poster for the modeling works in the GCIS-IMSAP project (Jin is first author), and an oral presentation on the exploratory visualization of earth science data with semantic web technologies. For the first one, David Arctur suggested that we may bring some geospatial components into the model framework. Stephan discussed that if we use GCMD keywords for GCIS, then in the GCMD keywords there is a part of it is for geospatial descriptions. While I was introducing the searching function in our plan for the GCIS-IMSAP project, Deana Pennington suggested we may also consider the user tag functions, that is, a reader can create tags in the NCA report for further use, while this may also be supported by some Semantic Web technologies. I also discussed the GCMD keywords with Tyler Stevens, a researcher in the GCMD keywords, on how to make GCMD keywords more open for use. He likes our feedback and already provided some information.
My oral presentation was based on some work originated from my PhD study. This work used datasets on the server of the British Geological Survey. I got some updates from Timothy McCormick, the Information Sector Manager (Geology) at BGS, on their Linked Data works of lithology. He suggested me to do some further work using their datasets and services. Luis Bermudez and David Arctur from Open Geospatial Consortium (OGC) suggested me to do more work on semantic web and Web Feature Service (WFS) and Sensor Web, and they suggested TW to obtain a membership at OGC to get fresh first-hand progress of OGC works.
AGU is a big event, a schedule is necessary, as those described above. And, there are also many other interesting side-events. Almost every day I crossed by some old friends, for some of them I had lost contact for more than seven years! The exhibit is great and I collected a bag of earth and space science cards, posters and toys for my son – is he going to be an earth scientist?
There is more to say about a seven-day conference with over 22000 participants. I have to stop here. For those issues related to specific research topics and projects at TW we will have further discussion in the separate groups soon.

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White House Visitors App, now on your iPhone, iPad, or iPod touch

November 9th, 2010

The Linked Open Government Data group has worked hard to make available US Government data as RDF, and over the past year they’ve introduced some really great tools for exploring government data. One of those tools, the White House Visitors app, is now a native app for the iOS product family. The native app provides live querying of the LOGD triple stores, queries DBpedia for more information about important people, uses the New York Times linked open data to find the latest articles, and pulls images using Freebase. For travel, the application caches data so that existing queries can be viewed when Internet connectivity is intermittent.

See the White House Visitors App on iTunes Preview or download it from the App Store.

Screenshots:


White House Visitors app finds the top 25 visitees (configurable) and lists them decreasing order.

Visualize the visitors and visitees in graphical form.

Using linked data, the White House Visitors app can find out more about people listed in the original dataset.

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Quick Update on ISWC Twitter Data (1)

November 8th, 2010

At ISWC 2010, there are several on-going efforts to leverage Twitter data. Some ones that I’m aware of are:

Joshua Shinavier has helped to build a triple store (powered by AllegroGraph) that contains tweets related to the conference, along with basic ISWC metadata. Here is an example of SPARQLing with the triple store (details about tweets with tag #iswc2010 and #iswc). More examples and guide on how to use the triple store will be out soon.

URL: http://flux.franz.com/catalogs/demos/repositories/iswc2010#query

Marian Dörk helped us to visualize tweets at ISWC. You can see the relative traffic by time, the distribution of buzz words at the conference, and who is twittering about what. Marian is looking into interviewing our attendees for the tool – if you have comment, let him (mdoerk@ucalgary.ca) or me know (baojie@cs.rpi.edu)

URL: http://ilab51.cpsc.ucalgary.ca/iswc2010

To be continued.

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Author: Categories: iswc, tetherless world, twitter, visualization Tags: