A call to science and technology to work on standards for environmental data sharing

Which recent Geoscience related journal article has most influenced your work?

For me it was Laniak et al. (2013) "Integrated Environmental Modeling: A Vision and Roadmap for the Future". With a BSc in Computer Science I had worked in the IT industry before I started in academia. When I read Laniak et al. (2013) my Geography Master’s I knew that that was exactly how I would want to apply my computational background. Laniak et al. presented a vison for the future of integrated environmental modelling. They called to science and technology to work on standards for data sharing, and envisioned web-based platforms for transdisciplinary community interactions. I knew that science is not only about observations and theory. But it was then when I deeply understood how the capabilities of modern computers support research, make it reproducible and, thus, can accelerate research. The potential of linking people and knowledge from different disciplines in order to jointly understand natural processes and to make decisions together overwhelmed me. This landmark paper has since influenced me throughout my PhD and beyond.

Reference:

Laniak, Gerard F, Gabriel Olchin, Jonathan Goodall, Alexey Voinov, Mary Hill, Pierre Glynn, Gene Whelan, et al. 2013. “Integrated Environmental Modeling: A Vision and Roadmap for the Future.” Environmental Modelling & Software 39 (0):3–23. https://dx.doi.org/10.1016/j.envsoft.2012.09.006

Staying informed with Literature Review on the smartphone

As a scientist / researcher you have to stay informed about the latest research findings in your field. Typically, this means that you should follow the publications of the most important journals in your research domain. I found that many researchers (including myself so far) only conduct proper literature reviews when they work on a specific problem, when writing articles and grant applications. Often they wouldn't find the time to go to all the journal websites and scroll through the article lists etc.

I recently discovered the Feedly RSS reader. RSS is long-known internet feed syndication protocol that is used to subscribe to updates on websites and blogs. I found that many, if not all journals, more or less provide RSS feeds for their latest articles, often with an abstract provided.  Feedly is a website application that helps you to organise RSS feeds and read them online. There is also an Android and an iPhone app. With these you can then read and manage your feeds on the phone. Now I quickly scroll through the latest articles every day via my mobile phone. This way it is just like scrolling through Facebook, Twitter or Instagram, but for journals. And the very few articles that you find relevant or that are of interest for you, you can save them in your Feedly backlog in order to read them later when you are in your office and take reading time :-)

Update: Inoreader is another very similar application to read your RRS feeds, and there are also the respective smartphone apps available.

One advantage of Feedly is that you can export and import lists of your RSS feed sources with so called OPML files.  OPML is available in many RSS reader web sites and applications, so you can both import and export OPML files of RSS subscriptions.

I prepared an OPML Export file for you, a standard list format for your feed URLs,  so you don't have to aggregate all the RSS URLs again. Happy reading and feel confident that you are not missing out on latest papers in your field.

Link to my export.opml file: https://www.dropbox.com/s/li0yjvwyt8cezsc/export.opml?dl=0

It includes links and feeds to the following resources:

• Information systems and information technology : nature.com subject feeds - rss url and webpage url
• Google Cloud Big Data and Machine Learning Blog - Google Cloud Big Data and Machine Learning Blog - rss url
• Research Participant Portal - Funding Opportunities - Recently published Calls - rss url  - webpage url

• Geography : nature.com subject feeds
• rss url = https://www.nature.com/subjects/geography.rss
• webpage url = http://www.nature.com/subjects/geography

• MDPI Water
• rss url = http://www.mdpi.com/rss/journal/water
• webpage url = http://www.mdpi.com/journal/water

• Hydrological Processes
• rss url = http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1099-1085
• webpage url = http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1002%2F%28ISSN%291099-1085
• Hydrology : nature.com subject feeds
• rss url = https://www.nature.com/subjects/hydrology.rss
• webpage url = http://www.nature.com/subjects/hydrology
• Journal of Hydrology: ScienceDirect
• rss url = http://rss.sciencedirect.com/publication/science/00221694
• webpage url = http://www.sciencedirect.com

• IJGI - ISPRS International Journal of Geo-Information
• rss url = http://www.mdpi.com/rss/journal/ijgi
• webpage url = http://www.mdpi.com/journal/ijgi
• Computers & Geosciences
• rss url = http://rss.sciencedirect.com/publication/science/00983004_OA/open-access
• webpage url = http://www.sciencedirect.com
• Springer Earth Science Informatics
• rss url = http://link.springer.com/search.rss?facet-content-type=Article&facet-journal-id=12145&channel-name=Earth+Science+Informatics
• webpage url = http://link.springer.com
• Transactions in GIS
• rss url = http://onlinelibrary.wiley.com/rss/journal/10.1111/(ISSN)1467-9671
• webpage url = http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1111%2F%28ISSN%291467-9671
• IJGIS - International Journal of Geographical Information Science
• rss url = http://www.tandfonline.com/action/showFeed?type=etoc&feed=rss&jc=tgis20
• webpage url = http://www.tandfonline.com/loi/tgis20?af=R
• CaGIS - Cartography and Geographic Information Science
• rss url = http://www.tandfonline.com/action/showFeed?type=etoc&feed=rss&jc=tcag20
• webpage url = http://www.tandfonline.com/loi/tcag20?af=R
• IJDE - International Journal of Digital Earth
• rss url = http://www.tandfonline.com/action/showFeed?type=etoc&feed=rss&jc=tjde20
• webpage url = http://www.tandfonline.com/loi/tjde20?af=R

Happy reading :-)

2017 startup day Tartu - some pics

2017 fieldtrip to soontaga fluxnet tower

The Soontaga station is an EDI Fluxtower installation of the Department of Geography at the University of Tartu, Estonia. We visited one nice winter day.  Later I built some scripts for the field researchers and physical geographers to check and export the data.

Source code: https://github.com/LandscapeGeoinformatics/fluxnet_daily_png 

External real-time graphs: https://kodu.ut.ee/~kmoch/fluxnet_daily/Soontaga_HFdata.html

A geeky intro into Fortran

On the 9th of  November I organised another local coding meetup. This time we got an introduction Introduction to Fortran and Forth in order to understand some of the origins of programming.

Our resident CompSci member Benson prepared and presented the materials and gave us a glance onto these two arcane, almost ancient programming languages. Yet Fortran is still very much alive and used in a variety of high-performance computing (HPC) scenarios.

You can use command line and a simple text editor (vi, emacs, nano, gedit, atom, notepad++, kate). For the faint-hearted Atom ( https://atom.io/ ) has most of the features we needed for this session, is open and cross platform.

Links to Fortran language standard and tutorial:

• Standards committee: https://wg5-fortran.org/
• Tutorial: https://en.wikibooks.org/wiki/Fortran_77_Tutorial

While Benson prepared a preconfigured VM for us, you can try out Fortran with a Gnu Fortran GCC installed by yourself, and maybe even Eclipse Fortran IDE:

• https://www.eclipse.org/ptp/
• https://www.eclipse.org/photran/

Links to Forth language standard and tutorial:

• Standard: https://forth-standard.org/
• Tutorial: http://www.complang.tuwien.ac.at/forth/gforth/Docs-html/
• Example simple interpreter: https://github.com/howerj/libforth
• Example interpreter for educational purposes: https://github.com/sayon/forthress

The materials are also collated on my GitHub account again. Happy coding :-)

Copernicus info session November 2017 in Tallinn, Estonia

On the 6th of November 2017, several Geoinformatics staff member of the Department of Geography and our international MSc in Geography/Geoinformatics students of the University of Tartu jointly attended the Copernicus Info Session in Tallinn.

The event was held in Tallinn in the conference rooms of the Building of Ministries as the eleventh in a series of national Copernicus events of the European Commission. We had several international visitors as well national estonian officials. For example we had the chance to meet with members of the Estonian Landboard, ESTCube and other innovative satellite data processing companies, and even the Estonian National Library.

One really interesting presentation was summarising the Sentinel mission really well:

After the event about the European Copernicus programme finished we used the "field trip" to visit the Tallinn old town, and we we did a nice walk in the event.

Online references to the event:

http://www.copernicus.eu/events/copernicus-training-and-information-session-estonia

and

http://copernicus.eu/infosession-estonia

A Python Pandas Coding Meetup

On October, 12th, I organised a local meetup event at the Department of Geography. We had around 15 attendees, both from Tartu industry and university students.

In this meetup we played with the Jupyter Notebook (http://jupyter.org/) and did some data wrangling with Python, Pandas (http://pandas.pydata.org/) and co., some data analysis and visualisation.

I presented on how we can use Miniconda, an encapsulated versatile virtual python environment installer, that works under the hood of the big Anaconda python distribution. Miniconda is basically a mini version of Anaconda that includes only the conda package manager and its dependencies. We used a Python version 3.4 because some of the libraries/tools we wanted to work with supposedly only are supported up to Python 3.4. Here it becomes obvious how practical virtual environments can be. They help you to keep various Python versions around without messing up your system.

After we had set-up our local Python working environment, I introduced the Jupyter Notebook. The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

I prepared a variety of resources that we worked through in the meetup. I shared the collated tutorials and course materials on my GitHub account, The repository contains a curated collection of Jupyter Notebooks of introductory materials about programming in Python in general, the Pandas data manipulation and visualisation toolkit, and the Geopandas geospatial library.

This repository aims at different degrees of experience with the Python programming language and Python data manipultation and visualisation libraries. Each folder contains a README.md (for the the online repository) and README.notebook.md (readme as readable Notebook) file that list the contents and some details for each of the 3 big modules here:

• 01 - Introduction to Python and the Jupyter Notebook
• 02 - Introduction to the Pandas library
• 03 - Introduction to the Geopandas library

In order to get started, download the full Meetup-Repositiry from https://github.com/allixender/meetup-notes/archive/master.zip and extract it to a LOCAL folder. Go back into the console/commandline prompt and change into that folder. There you should then start the Jupyter notebook.