BioGeomancer...and other sources of Georeferencing

Over the past 250 years, biologists have gone into the field to collect specimens and associated environmental information documenting the range of life. The results of these explorations are an irreplaceable archive of Earth's biological diversity that plays a fundamental role in generating new knowledge and guiding conservation decisions. Yet, roughly one billion specimen records, and even more species observation records, remain practically unusable in their current form. Georeferenced biocollection data is in high demand. Mapping species occurrence data is fundamental to describing and analyzing biotic distributions. This information is also critical for conservation planning, reserving selection, monitoring, and the examination of the potential effects of climate change on biodiversity. Increasing the availability of georeferenced species distribution data will vastly increase our ability to understand patterns of biodiversity and to make balanced conservation-related decisions. Most data in these analyses come from natural history collections, which provide unique and irreplaceable information, especially for areas that have undergone habitat change due to clearing for agriculture or urbanization. (source) BioGeomancer is a tool that provides a Geo-referencing service for collectors, curators and users of natural history specimens...I guess that's where GIBIF started from.. It seems like the Workbench was completed in 2007. It was using three existing applications, BioGeomancer Classic, GEOLocate, and DIVA-GIS. By browsing in this site I have a collection of many Geo referencing sites other than GIBIF: One that will probably seem useful to me as a marine scientist is the OBIS:Ocean Biogeographical Information System. An other one is the MaNIS:Mammal Network Information System, which we can use in our New Mammals phyloinformatics project.. and other sites such as ORNIS, or REMIB.

Seeing the Great Barrier Reef from our couch...

Millions of people will be able to dive on the Great Barrier Reef thanks to a ground-breaking expedition. The Catlin Seaview Survey will upload on Google Earth about 50,000 panoramic images of the reef. When those images are merged, it will feel to people like they are virtually diving in the Reef! (source: www.heraldsun.com.au - February 24, 2012 10:04AM) ahh... so amazing... Can I work here?? :-)

Bio-hacker..

Today I had a 6 hour seminar on office Access in the Library of Glasgow Uni.. and I was wondering all day... Why? Why is there NO free software for pdf conversion to excel or access??? ..After a small google search and some downloads, I found this program called "Able2Extract", which was not too bad for a simple conversion.. but as my friend Dominic described in his blog, our data was still not merged into the cells, so we either had to do it manually, since excel can't keep all text while merging.. or..try and find another way to do it... So I thought I'd experiment a little... first I tried to hack :) the trial version (sshhhhh) Just in case the full version had more options... no success...

I tried to figure out what to do with defining the rows and the columns in each page.. But it had to be done manually, and still needed cleaning in the end ..

After browsing to different sites and some free downloading of trial version programs, I got the most clear result by using Nitro PDF Professional online, which e-mailed me the file with the converted PDF into XLS format.

The data definitely needs more work.. so manual copy - paste can't be avoided... Why am I doing all this?? - Forgot to mention earlier about our Phyloinformatics project decision. We agreed with my friend Dom what we will both work on the New Mammal data provided by the paper published by D.M. Reeder, K.M. Helgen & D.E. Wilson (2007) "Global Trends and Biases in New Mammal Species Discoveries". We will try and apply as much as possible from everything we learned in the phyloinformatics course. We talked about doing all kind of analysis. For now we will clear up the data in the excel and create a fusion table and work with that, while doing some background reading on methods for defining new species. Dominic also uploaded his cool ftw blog http://natureftw.blogspot.com/ so we'll both be reporting our everyday phyloinformatics concerns... Goodnight world of blog.. tomorrow, hopefully more posts of our project evolution..

“The affinities of all the beings of the same class have sometimes been represented by a great tree . . . the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.” Origin of Species, Charles Darwin (1859)

Bees can dance, that's for sure..but can they sing too??

Well, no.. bees have not gone crazy yet. But there are interesting news for the world of Taxonomy..

A horse fly with a golden booty has been named after the “Bootylicious” singer herself — pop star and new mom Beyoncé, as the NY Daily news report. The previously unnamed species is now called Scaptia (Plinthina) beyonceae, in honor of the singer, according to a press release from Australia’s Commonwealth Scientific and Industrial Research Organization (CSIRO). Researcher Bryan Lessard says the fly’s gold hue makes it the “all-time diva of flies.” “It was the unique dense golden hairs on the fly’s abdomen that led me to name this fly in honor of the performer Beyoncé as well as giving me the chance to demonstrate the fun side of taxonomy — the naming of species,” Lessard said. Wikipedia also seems to be updated to this new-named specie... and interestingly enough, it also includes a huge list of organisms named after famous people!! How cool is that?! :)

Shark-A-Talk...

Today was another fun day.. We decided to cook special dinner with a couple of my Glasgow friends.. some of us in Biology and Environmental Sciences and some in Geography.. we all had some very interesting conversations... one of which included sharks!! Sharks can be pretty scary.. we all have seen them in the movies.. but are they really scary?? ..if you think about it.. they are more scared of us... and generally, Sharks are not a threat to humans! but Humans are a threat to sharks!....or maybe Octopus are... haha.. pretty cool hu?...but anyway..

Generally, I find them fascinating!!.. I remember one of my Ichthyology class labs in my undergraduate, where we had to do a shark anatomy. The surface of their skin has an amazing texture.. I can still remember what it felt like when I first touched it. No wonder why people are Biomimicking Sharks... ..but the point was that while talking about sharks, the presence of sharks in Greece came up in our conversation and it made me think.. what species of sharks do we have there? and is there a dangerous species that we should be aware of?...Searching for shark attacks in the Greek waters I found some interesting information... I never thought Greek waters could have any chance of shark attack to human. I've always swam thinking I was 100% sure a shark wouldn't attack me.. because when I was a kid, my mom always told me.. there are no sharks in Greece!! But as a biologist, I found out that there are plenty of Mediterranean Shark species..and some of them love swimming in the Greek clean blue waters. So I found out that there are 47 different species of shark inhabiting the Mediterranean Sea.

Archipelagos a Greek marine research organization seems to have some interesting facts and pictures of sharks caught in the Greek waters. They also discuss certain issues about a number of shark species being in danger. Once again I got lost in the world of internet trying to find further information about Greek sharks.. Greek politicians would be considered a dangerous shark species...but we obviously can't fit them in the phylogenetic tree of sharks. An interesting database for sharks was found in this site: http://www.shark.ch/ ...I won't use it today, but I think it might be a useful site for further reference. I'll definitively need to look up some of the species one day, or maybe use the data to make a tree.. Later I tried using iSpecies and searched for a couple of species that were found in the Mediterranean, but also found in Greek waters. Looking at their distribution in GBIF, for most species I looked for I could not see dots in the Mediterranean Sea, and I could not find any distribution around the Greek waters, so that made me wonder.. Is GBIF not collecting data from researchers in Greece? or is it just that there is no shark data from that area? ...because obviously sharks are found in Greek waters (M.Karagiannis, 2009)..

Intro to Taxonomy

Looking for the best phyoinformatics project, I started with reading some historical background about taxonomy in general; In the library I found this small book, titled: "Animal Taxonomy" by Theodore Savory, published by Heinemann Educational Books Ltd in London, 1970 (so it's quite old). However it includes great information on the ways to approach systematics and how taxonomy and the classification of organisms can help science. So, have we ever wonder.. 'Why classify?'- Classification is forced upon us by the limitations of the brain (Savory, 1970). Generally some believe that the human brain classifies instinctively and unintentionally. Classifying is considered as an innate mode of thinking and leads to a study that reveals both difference and similarities between the objects concerned (Savory, 1970). In science the need for classification is even more important. Phylogenity is considered as the imaginative side of theoretical zoology. It's main subject is evolution of animals and the objective of the scientists is the tracing of evolution. Therefore, the science of taxonomy is not aimed to classify the organisms, but also to look at them in depth, figure out their past, compare them and decide whether their differences are due to adaptation needs into different environments and whether the similarities are the result of a common ancestry or of convergent evolution. In two words systematics can just save ourselves from zoological chaos. ...and it's a true chaos if one thinks about it. There are so many organisms to include in the tree of life, that it would take us so much time, if every time we would need to present a tree of an organism we would have to do it by hand. Therefore, we can see a large progress made by classical taxonomy itself, which necessitated the introduction of new methods of analysis and new approaches to synthesis. Technology has made a significant progress, especially the last 10 years, while everyone has an easy access to the world of internet. Technology has helped taxonomy to evolve in an impressive extent. Data obtained from places all around the world are shared among scientists. Integrated data may help us learn many things we don't know. Nowadays we find many sources in the internet with load amounts of information. Combination of these sources can give us the best results. Choosing the best project for this class is challenging since there are so many aspects to think about and a couple of published papers to look through. I might be able to combine two of the projects suggested.. I still need some time to think about it..