Spent a lot more time with drupal - and I would need even more!

It seems like it has taken me forever to complete the assignments for Week 5. Not only did I attend the Biodiversity Informatics Workshop in Nairobi right as Week 5 was starting, but I also got sick on the way back from Nairobi and had a very unproductive week getting checked out. I'm almost back to full speed, but this week's installations and learning curve for all the settings that go with the installations has left me somewhat dazed, confused and stressed about trying to take it all in.

My overall impression is that drupal is very useful, but takes quite a bit of time and expertise to run well. It does not seem like a completely natural fit for a digital collection of photos, video and various text formats. It can be made to work for that, but since I haven't spent a lot of time working with it, my intuition would be to continue to search for other solutions that might be a more natural fit. On the other, hand, I would also want to do some research into the popularity of drupal compared to other solutions and also see how big and active the user communities are for an assortment of content management systems out there right now.

One example of where I'm at with drupal involves the installation of the lightbox2 module. It was certainly easy to install. I had no problem just basically downloading it and moving it to the modules folder in drupal. On the other hand, even though lightbox2 is installed and apparently running quite nicely, in order to actually use it, I need to modify some html for the links to images. I did a quick search in the drupal.org site and could not find any examples of how to do this. There are so many moving parts to drupal that I can't seem to determine where I would start looking for a way to add snippets of html to image links. So, I'm stuck for the time being. It would be nice to have better documentation for this kind of thing, but since the lightbox2 module is basically free, with the developer requesting some financial support to keep developing it, I don't expect to get support that way. Perhaps if I were better integrated into the drupal community, I would know where to turn.

So, I'm glad that I have spent so much time with drupal the past few weeks, but I'm also going to be interested in seeing what else is out there - I saw something about DSpace, I think. It should be interesting!

First evaluation of Drupal

The question this week is about how well drupal might meets my needs in producing an online digital collection. From this week's exercises, I am far from expert in this area - just a novice, really, so take it all with a grain of salt, just as I do right now. Still there are general impressions and it can be good to have fresh eyes looking at a situation or proposed solution for a problem such as this one.

Drupal is not hard to install at all. Once you have the basics figured out, one can get drupal running. I have not configured it to run connected to the internet, but I'm hoping that would not be too difficult. On the other hand, I find the interface to be pretty clunky compared to what I am used to using in terms of software. You have to know where you are going and what you are doing or you may not get there or get it done. It would be nice to have something like an inspector window that allows easier navigation through the drupal features and interfaces. It isn't really that hard to do things, but I don't like having to click back and forth - in and out to do things that are within the context of the window I'm currently in.

As far as displaying digital images, drupal surprised me by not choking on some of the file formats I threw at it. It handled my DNG RAW format fairly well. It didn't know to rotate the preview, which is actually an embedded JPEG, but that's no big deal, really. I think that imageMagic or some other plugin could take care of that problem. It did get to be a hassle to have to add various common image formats to the list of importable items, but I suppose once you got the hang of that, you could always anticipate it ahead of time.

It does seem that there are so many easy ways to display galleries of images out there though. I wonder if there might be better Content Management Systems that have taken a cue from such gallery software available from Adobe, Apple, Microsoft, et al. If not, I think there should be. I've brought up the topic of being able to leverage the embedded metadata in images for use in these galleries before and I'll beat the drum again. The model of having to move metadata around separately from the image files themselves just strikes me as primitive and inefficient. Something I'm going to have to look into a lot more, I suppose.

More from the Biodiversity Informatics Workshop

There are some amazing databases and digital collections available in the biodiversity realm. I wanted to share some of the more impressive sites that I've learned about in the past 10 days, so here goes:

http://atrium.andesamazon.org/ - this technology platform is sponsored by Gordon and Betty Moore. If you've ever heard of Moore's Law - this is the guy who came up with it. He's also a big believer in maintaining biodiversity on planet Earth. It's nice to have smart friends who also have money and are willing to put it to good use. Check out the amazing work that is being done in the Amazon basin at http://www.andesamazon.org/. The field researchers are actually uploading data on a real time basis via satellite feed, allowing the data to be ingested and shared with scientists all over the world who can collaborate with the people on the ground. It's truly an amazing technological feat.

Another cool site which contains a lot of digital resources is from the American Museum Congo Expedition 1909-1915 at http://diglib1.amnh.org/. Just for fun, go to Advanced Search and enter monkey in the description field and search. Just to the right of the Red colobus monkey look for the View Related Field Notes link and click that. Now click on View Field Note and you can see the original hand-written notebooks of these scientists. Okay, a little too many clicks to get to what you want, but it still is a fascinating site. There's lots to explore and some of the content is organized into pre-set Galleries to get you started. I found it really interesting stuff.

Another interesting development is in the area of specialized Content Management Systems for sharing biodiversity information. We had a presentation from a Dutch company that is developing these for use worldwide. These "Bioportals" are based on simplenews CMS, which is called a lightweight CMS. See an example of it at http://www.nlbif.nl/. There is another site, which is down at this time for Tanzania at http://www.tanbif.or.tz/. The site is frequently unavailable, at least from my sporadic and slow connection in Nairobi of late. The promise of sharing information over the internet is real, but for much of the developing world, there is also a pressing need for basic infrastructure to support such exchange. It's going to be a while before the whole world can even access the internet reliably, which will make these kinds of sites dependable resources for research.

Since we have been discussing digital repositories, take a look at what's happening at data basin http://www.databasin.org/. It's a repository of spacial information that also has tools for the use of the data and facilitates a network of scientists and practitioners. There are dataset areas on the site that have been focused on Climate, Boreal Forests, Aquatic and Protected Areas. It seems to be based on some kind of CMS, but I'm not sure which. It does have a lot of interesting content and I found it quite engaging even as a non-biologist.

This week we spent a lot of time with Geographic Information Systems. It's a fascinating area and we had the good fortune to have a U of A PhD candidate named John Donoghue to walk us through the basics of GIS. Today, he even had us working with climate change data for the year 2080 and seeing how it would affect certain species. I did mine on pan troglodytes, the chimpanzee. I could see how the chimp's habitat was projected to change in the next 70 years by using graphics in the Q GIS program and MaxEnt. I feel pretty enthused to have even a rudimentary command of the tools needed to do this. I hope the Workshop will help move us toward a more sustainable environment for the chimp, as our nearest relative. Maybe I should do a projection on the species homo sapiens next time.

Photos from the Biodiversity Informatics Workshop in Nairobi, Kenya

Photos from the Biodiversity Informatics Workshop in Nairobi, Kenya. I can't seem to figure out how to put captions under the photos, so I'm just going to leave a bit of information here. Baboons and warthogs roam the grounds of the Multimedia University College of Kenya, Nairobi, Kenya. You see them most mornings and evenings around campus. You can also see a group photo of workshop participants and some classroom photos.

Jambo from Nairobi!

Between some pretty severe jet lag (10 time zone changes) and the sporadic internet access at the facility where we are staying, it has been a challenge to do anything more than the approx 8 hours per day workshops here at the Biodiversity Informatics workshop, plus getting around, eating, etc.. We are staying at the Multimedia University College of Kenya on the outskirts of Nairobi, which was built in the early 1960's on the other side of the road from the Nairobi National Park, which has lions, rhino, antelope, etc. We can see baboons, monkeys and warthogs wandering the campus in the mornings and evenings.

The workshops are covering a vast, and I do mean vast amount of material about Biodiversity Informatics. This past week, we have covered the following Biodiversity Informatics topics:

Fundamental Principals

Standards

Biodiversity Databases (one of my favorites so far)

Example from Congo Expedition exporting Darwin Core

Brahms database (botany)

Specify (species ID)

Plotting GIS coordinates using Google Maps and Google Earth

Catlogue of Life (e-infrastructure for dynamic harvesting of data)

Biodiversity Mapping / Bioportal toolkit

Fusion tables

Web access tools

Content Management systems (a great presentation about Drupal)

Yesterday, we went on a field trip to the National Museums of Kenya, which is in downtown Nairobi. We passed by one of the worst slums of the world on the way - Kiberia slum is notorious and we are advised to stay well clear of it. Once we got to the museum, we saw how plant specimens are processed for intake into the collections there. The plants and insect collections are both well into the millions. The National Museum is hard at work migrating data from hard copy to electronic, or soft copies. We also got to take a look at the bird, mammal and fish and reptile collections. I was amazed to see a huge tank in the back of the fish and reptile area with an actual specimen of a coelacanth, which has been called a living fossil or Lazarus taxon, because they seemingly came back to life. They were thought to have been extinct for something like 65 million years, but one was caught and identified in 1938 and several more have been caught since then.

At any rate, the real-life examples of how the Museum of Kenya staff are using Bioinformatics to increase the value of their collections is really exciting. I'm going to try to figure out how to post some photographs from the workshop thus far. It looks like I just have to click a few buttons - but for now I'm off to the next workshop - I think it is on Geographic Imaging Systems, and then we will go to the African Conservation Centre to see their GIS labs in action. They are tracking elephants and studying the ecology in elephant habitat.

A lot on my plate

The combination of the technical and management sections of 675 definitely add a level of complexity to my already scattered life these days. I also think that the design of the d2l site adds to the confusion when it could be part of the solution. So many different things one has to click on and maneuver around to get to where one want to go. I would love to be on a redesign team for d2l!

The subject matter is very interesting in both areas, but I definitely feel that I am approaching maximum data input limits these days. I'm sure it is a combination of all the various commitments I have with family, work, school. There is very little down time to just contemplate what I am reading - which makes it harder to write. I also miss the face-to-face interactions of the old days - asynchronous conversations are very convenient for a busy schedule, but there are so many things missing from the conversation. I feel like I am missing the chance to really know the other people in my class and I know it would really be interesting to do so.

The technical stuff is not as difficult as 672. I do have to brush up on things and go back and double-check on a command or such, but generally that part is feeling more comfortable - the complexities of the readings and concepts there are getting tougher at the same time. It's going to be interesting to keep up with it all when I travel to Kenya for the Biodiversity Informatics workshop with a group from SIRLS including Director Dr. Bryan Heidorn. I hope I can find good internet in Nairobi!

Deciding on a digital collection

One of the first assignments in IRLS 675 is to gather a digital collection and to discuss what it consists of, what it is about, who might access it and some terms that might be used to provide access to the collection, in case someone is actually looking for such a grouping of digital stuff.

I'm going to go with the first thing that comes to my mind: I have a lot of photos of Mission San Xavier del Bac from a book project but also from other work that I have done there over time. I also have some video I have taken there and a DVD that was done by KUAT-TV about the work I did there. I also have some links to websites that are about San Xavier and some text files (depending on how public this will be, I might need to get permission to use some of the textual information, which I don't have rights to distribute myself). Which brings up the question of copyright and how it might affect this project. Depending on how we will distribute or provide access to the collections, do we have the right to use digital objects that we have not authored ourselves? Well, I know the legal answer is that we don't, but as a practical matter I suspect it will happen and happen a lot. But I digress.

This collection would be of interest to people who are interested in art, religion, architecture, history, culture, the southwest, photography, painting, sculpture, and all of these as they relate to Arizona and Tucson, in particular. Those might be some of the terms that would be used to access it, as well as the details involved in what is being captured in the images and text.

I'm a bit behind on things this week due to the amount of time I have spent preparing to travel to Nairobi Kenya to assist with a Biodiversity Informatics workshop there as a representative of the United States. I applied for a "scholarship" and am honored to have been one of the four chosen to go, but there was a lot of work to do to apply for a visa and get vaccinations just to start to get ready. Still, I think it will be a great learning experience both academically and culturally.