Categories
biology notes

Newspiece about the Cifonauta database

Reportagem sobre o Cifonauta no Repórter ECO da TV Cultura.
Categories
notes biology imaging

Sea biscuit metamorphosis on the Node’s calendar

The sea biscuit metamorphosis image that I submitted for the Node’s intersection image competition was selected for the November calendar! You can download it here.

Sea biscuit metamorphosis.
Categories
biology notes

Newspiece about the exhibit Ocean: Hidden Life

Reportagem sobre a exposição Oceano: vida escondida na TV Cultura.
Categories
articles biology

Turtles, embryos, and fossils

I wrote a text about the development and evolution of the turtle shell on The Node: Turtles in a nutshell.

800px TurtleOmaha
Turtle at Henry Doorly Zoo, Omaha. Photo by Algy3289.

It shows the beginning of shell formation in embryos and how this can help us understand the evolution of such unique body pattern. 3D animations and fossils are included!

Never thought I would post a vertebrate on this website… but having shoulders inside the rib cage made me make an exception, poor things :p

Categories
articles biology code

Living Bibliography

Living Bibliography was born when, a few weeks ago, on a Saturday morning, I bumped into the Hack4Knowledge, a meeting to build apps, tools, and remixes with existing databases to innovate and enrich the creation and dissemination of knowledge.

I was already playing with the Mendeley API and took the opportunity to put an idea into practice: aggregate bibliographic references related to a taxon. It is not a particularly new idea, and it also does not differ much from searching a taxon name on google or Scopus, but since the Mendeley database is based on its users’ collections, it is possible to extract some interesting information. For example, find out which articles are more popular or create trending topics with popular taxa based on the number of readers and related publications.

Living Bibliography homepage
Living Bibliography homepage

Regardless of the source, article data also allows extracting useful information such as the most active authors on a certain taxon, network of collaborators, annual variation in the number of related articles, popular research topics for each group, etc. Integrating the data and using visualization tools it would be possible to “see” holes in the knowledge or follow the history of one’s research.

Imagine if every article was freely available with contained information (metadata) about the studied organisms with taxonomic classification, occurrence data, collection sites, dna sequences, citations with semantic markup, research topics, hypotheses to test, methods, raw data, etc. Anyone would be able to have a summary of the current knowledge about an organism. Especially interesting to set research quidelines and avoid spending money with the same mistakes; optimization of science. And do not forget about the possibility to attach observations, annotations, discussions, unsolved questions, and other collaborative activities.

Well, after creating a prototype of the idea, I have just pust the basic functions of the aggregator to work. Nothing I wrote above is included, just a search interface where you can use a scientific or common name and a page for each taxon with a list of related references and some sorting options. If a taxon is not in the database, it searches in realtimes, therefore, it is necessary to wait for a little while and reload the page (at least until I automate this).

Taxon page in Living Bibliography
Taxon page in Living Bibliography

If you are interested you can test the Living Bibliography at livingbib.brunovellutini.com. Just remember it is completely experimental, I do not guarantee that your favorite articles will appear or that the information will be accurate (there are many duplicated articles, wrong author names, badly formatted titles, swapped journal names, and so on at Mendeley). I don’t know how much I’ll be able to work on it, but the source code is open and I would love to hear ideas and suggestions :)

Categories
biology imaging notes

Pluteus larva

Pluteus larva of the sea biscuit Clypeaster subdepressus.
Pluteus larva of the sea biscuit Clypeaster subdepressus.
Categories
biology imaging notes

Metamorphosis of a sea biscuit

Metamorphosis is a dramatic life-changing event for many invertebrates. It’s the intersection between two distinct lives – larval and adult. It is how a caterpillar becomes a butterfly.

The process is fascinating, specially when you have the chance to see it happening with your own eyes. You too can see it in the video A Sea Biscuit’s Life.

Recently the community website the Node from The Company of Biologists announced a thematic image competition. The images needed to be related to developmental biology and some sort of intersection.

Because intersection is essentially another word for metamorphosis, I submitted a photomicrograph of a metamorphosing sea biscuit from my master’s thesis research. It made it to the final and was a runner-up!

Metamorphosis of a sea biscuit.
Metamorphosis is a drastic (and common) event in animal life histories intersecting larval and adult stages. The photo shows a sea biscuit during metamorphosis. The apparently amorphous mass of cells exposes the duality of this transformation moment. The larval body retracted and lost its form, but larval skeleton spicules are still attached (at the top). At the bottom developing podia and spines already move and interact with the substrate as the sea biscuit learns how to walk its first steps.
Categories
notes biology imaging

Young sea star

Young sea star
Oral surface of a young sea star. 5th place in the Nikon Small World 2009.
Categories
notes biology

Enigmatic echinoderms

Enigmatic echinoderms
Seastar Luidia senegalensis (photo by Alvaro E. Migotto). Cifonauta marine biology image database http://cifonauta.cebimar.usp.br/media/9724/

I also here salute the echinoderms as a noble group especially designed to puzzle the zoologist.

Book: The Invertebrates: Echinodermata (1955)
Author: Libbie Henrietta Hyman
Page: Preface
Categories
biology articles music

Dream Sequence

This is the music video I made for the song Dream Sequence by Professor Kliq using the images of my master’s thesis on sea biscuits.