Some of the Sightings @ the Isle of Mull

GREAT experience!!! :D

Plastic bottle fish sculptures on Botafogo beach

Plastic bottle fish sculptures on Botafogo beach

Harvest flies

This topic is a bit irrelevant, non-marine and non-phyloinformatics.. but climate change and temperatures issue is a maojor part of my dissertation topic... It's probably my first June I feel so cold, I even miss the sound of harvest flies... So I couldn't help but wonder...Have we seen any changes in harvest flies due to global warming?? After a quick research.. I couldn't find a decent paper and research on Tibicen canicularis. But I did run into this video again, reminding me that it's probably not the last June that I can't hear the Harvest flies sing (and not the grass hoppers as referred in the video.

Can Fish Remember???

MindGenius Mind Mapping Software

This is Genius!!! I wish I had explore that earlier... It looks like a really good software for brainstorming and capturing ideas and later presenting them. I will keep it for a further reference.. it looks like it will be very useful for my project. I could have been useful for my phylogenetic trees for my phyloinformatics project...oh well..when I use the free trial, I will add a comment on it..but other comments on the program are also accepted. :)

NCBI_Blast_Tree

The process of making a phylogenetic tree is simple in essence, however in our case, where we had to deal with many new species; to make a proper molecular tree would be a challenge. The basic steps involved in creating a tree from molecular sequence data are: (i) Some collection of sequences obtained from the NCBI database by a BLAST search and (carefully) aligned to put together homologous residues, nucleobases, or amino acids in case we want to compare proteins. (ii) Identifying other sequences that are related to the sequence of interest and obtain the data for that sequence is also a crucial step. (iii) Aligning the sequences and finding the differences between all pairs of sequences would be our next step, we would use ClustalX in order to accomplish that step. (iv) Using the alignment results, we can generate a phylogenetic tree. (source: "Phylogenetic Trees Made Easy - A How-To Manual for molecular Biologists" - Hall G. Barry) Our first step was to Refine our data table and find the NCBI codes for each specie.

Filtering our data for all the species that have a NCBI code.

As we can see, most of the species did not include a valid NCBI ID code, since they are still new species. Another reason could be because of a spelling mistake in their scientific name, are because the same specie could be know with another scientific name, causing a confusion. While filtering the data, we got only 100 species that contained NCBI ID number, out of 328 species in the list. And only 70 species had both NCBI and uBio ID names. I've decided then to look in NCBI Taxonomy database for a small group of new mammals and compare them and try to make a good molecular tree for this small group. Unfortunately it was very hard to find sequences of the same protein or molecule in each of the species and then make a sequence alignment with ClustalX. ..... The best tree I could manage to find is a typical tree in NCBI, where I used the NCBI codes that I had produced in Google Refined table. NCBI Tree

In our Data, only 169 species appeared with NCBI codes and these came out to our Taxonomy Tree in NCBI. Dominic and I tried to save the file in different available formats. Unfortunately, we do not know how to open this file after we save it. We tried using PHYLIP, since Dominic used that while attempting to make a tree, but it didn't work for some reason.

Errors...

I have downloaded and tried many of the programs I found in this page.. Even though I was hoping to work with TreeView and figure things out.. Treeview wasn't very friendly to me. I tried to follow the instructions given in the manual and while I was trying to make a taxon list and load it to the program, I would always get an error for some reason. I also tried to paste a nexus script example, but still wasn't working. I uninstalled the program and installed it back again...nothing. So, I gave up and looked for something else. Then I worked a bit with NDE, but I couldn't really understand what was it producing.

Ahhh... ok lets take it from the start. I am forgetting what I have done in the first place while I search stuff, get lost from one link to another, stick on errors and then can't remember where I began from. First step: BLASTING the Cricetidae family.. We're getting a good looking result, but it's not what we need..I feel lost, need to revise my course notes again.