Author: ArilabAdmin

SWARM 2019

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This year, our lab co-organised and hosted SWARM 2019: The 3rd International Symposium on Swarm Behavior and Bio-Inspired Robotics, bringing together 160 biologists and engineers from around Japan and the world. The theme of this conference, which has been held in Kyoto twice before, is to promote interdisciplinary interaction between biology and engineers within the realms of collective behavior and bioinspired design.

We co-organized (with Christian Peeters) a symposium within the conference, “Engineering Insect Morphology by Natural Selection” to highlight recent research from understanding how insects work to inspire robotics. From our lab, Evropi Toulkeridou presented her research on the automated segmentation of micro-CT images by deep learning. In the same session, Adam Khalife, a former intern (now a PhD student at IEES-Paris), talked about his work on the muscular and skeletal structure of worker ants.

Other talks included Christian Peeters (ant thorax), from Yuko Ulrich (collective behavior) and Adria Labeouf (social circulation), and Hitoshi Aonuma (trap jaw ant mechanics). Evan wrapped up the session by asking how the endless engineering solutions of nature, currently locked up in museum collections, can be utilised to its maximum potential to inspire human innovation.

We hope that the symposium provided a fertile ground for biologists and engineers to exchange ideas and develop collaborations.


Thank you and otsukaresama to all the volunteers and especially to Chisa for her hard work organising the logistics!

Augment your reality with some new ant species- in 3D.

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Ever wanted your taxonomic revision with its own custom-made iphone app?

Here in the lab we are always looking for ways to make taxonomic work more exciting and engaging, and we believe that technology can help us connect people with biodiversity in new ways.  We have previously been exploring the use of 3D x-ray imaging for enhancing taxonomic revisions (remember the dragon ants?).  But one nice thing about 3D imaging is these data can travel to many endpoints, everything from an image on your computer monitor to a physical 3D print or to virtual or augmented reality. 

3D ant model in augmented reality

We were wondering how augmented reality might help enhance taxonomic revisions, and scientific papers in general.  Imagine as you flip through a paper 3D figures and images pop out of the page and float on your desk.  How much more exciting would that be as a way to experience new species?

Some time ago, Eli Sarnat and many of our lab members decided to revise the Fijian Strumigenys, just a little project to organize one of the coolest endemic radiations in Fiji and describe some new species.   But to push it further, we thought we would see if we could do it with augmented reality enhancement.  After lots of testing and looking around, we hired an app dev team based in Ukraine to code us up a custom app to display species models, 3D rangemaps, and automatically project 3D figures.  The result, Insects3D, can be downloaded at the app store for iphone.  Check it out, especially while reading the open source paper from Insect Systematics & Diversity.  While primitive and not at all simple or fast enough to achieve for all taxonomic works, we hope it shows an inkling of what’s possible in the future.  Let us know what you think!

3D model of a new species, Strumigenys avatar, floating above the plate in the paper

Read the Paper

Download the app

Congrats, Graduates!

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Congrats to Patricia Wepfer and Yafei Mao, the two latest PhD graduates from the lab!  Patricia is back in Switzerland working on a project at ETH Zurich, but came back for OIST graduation, and Yafei is about to leave for a postdoc at the U. of Washington.  Both Patricia and Yafei did great PhDs on coral evolution. Corals aren’t very ant-like, but we like them anyway.

Yafei and Evan
Patricia, Evan, and Satoshi Mitarai, her other advisor
Patricia signs the great ant of success (aka Strumigenys nidifex)

We had a signing “ceremony” with Patricia, Yafei, and Cong Liu, the first lab graduate from last year and is about to leave to be the E.O. Wilson postdoc at Harvard. 

Congrats everyone and Gambatte at your new jobs!

Welcome New Lab Members!

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We are pleased to welcome three new arrivals to the lab recently.

-Jamie Kass (left) is starting a term as a JSPS postdoctoral fellow coming from the US. He is an expert on species distribution modeling and one of the lead developers of Wallace. He is going to be working on our OKEON community monitoring data and also collaborating on other projects related to global biodiversity.

-Fumika Azuma (center), also coming most recently from the UK where she recently got a bachelors in geography from UCL, is the new technician in the lab. She has actually been here for a while as a research intern, but we liked her so much we convinced her to stay. She will be working on a range of tasks, but especially GIS, insect collection curation, micro-CT, and molecular work.

-Kosmas Deligkaris (right), coming from the UK, has a background in neuroscience and is now a computational specialist who will be working on computational support, data and database management, server admin, workflow design, and other related projects for the lab.

Welcome everyone and Gambatte!

Open Research Technician Positions

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Note added Jan 2019: These positions have been filled. Thank you for your interest.

We’re hiring!  Please see the ad below and get in touch if you are interested:

The Economo Lab (http://arilab.unit.oist.jp/) at the Okinawa Institute of Science and Technology Graduate University (http://www.oist.jp/) is seeking qualified applicants for two technician positions.  The lab works at the interface of ecology, evolution, and natural history, with an empirical focus on ant biodiversity.  We use a variety of approaches to understanding biodiversity including field expeditions, collections-based research, x-ray micro-CT, 3D modeling and morphometrics, phylogenomics, biodiversity informatics, and quantitative theory. Although two positions are described below, we are flexible with regards to division of duties among the two hired individuals.

RESEARCH TECHNICIAN:

Description:  The hired individual will get involved with a number of research activities in the lab including: curating an entomological research collection, managing lab databases, procuring lab supplies and materials, and performing miscellaneous tasks to support lab research.  In addition, there are exciting opportunities to become an expert in X-ray micro-CT scanning and downstream applications such as segmentation, 3D modeling (e.g. see our gallery online), morphometrics, 3D printing, and interacting with biodiversity data in virtual and augmented reality.

Qualifications: An undergraduate degree or higher in a scientific or technical field and experience with scientific research are required.  Although there is no requirement for proficiency in a specific computational program/language, it is important that the person has strong computational skills and a high ability to learn different software and methods independently. Although not required by any means, experience with any of the following would be highly desirable: biodiversity collections management, 3D modeling, 3D animation, data management, computational phylogenetics, geometric morphometrics, GIS, HPC, VR/AR applications.

RESEARCH COMPUTING TECHNICIAN:

Description:  The hired individual will be responsible for computational support of lab research including; designing and maintaining research databases, maintaining lab websites, assist with design and maintenance of bioinformatic data analysis pipelines, application support for utilizing HPC resources, and desktop support to lab members.  In addition, there are opportunities to lead or participate in development of new technologies that facilitate and accelerate biodiversity research.

Qualifications:  An undergraduate degree or higher in a scientific or technical field and experience with scientific research computing are required. As this position is not tied to a single application or task, the ideal candidate would have a good baseline of programming skills, including familiarity with both compiled and interpreted languages, and ability to learn independently. Proficiency with Linux, SQL-based database design and administration, and at least basic familiarity with server administration are required.  Experiences with one or more of the following would be highly desirable but are not required; GIS, bioinformatics, phylogenetics, ecoinformatics, parallel computing, and statistical computing

Job Data:  OIST is a newly established international graduate university located in the resort area of Onna-son, Okinawa, Japan, and offers a high quality of life and good working conditions in an international environment.  Logistical and financial assistance with relocation will be provided, along with a competitive salary and benefits package.  OIST is an English-language working environment, so knowledge of Japanese is not necessary.

To apply, please send a cover letter, CV, and list of three references with contact information to <economo@oist.jp> in an email with subject “Research Technician Application” or “Research Computing Technician Application”, as appropriate.  Informal inquiries are also welcome at the same address. Application review will begin immediately and will remain open until the positions are filled.