Website update

Author: sjmgarnier

Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 gem 'github-pages'
 gem 'json'
 gem 'rouge'
-gem 'wdm', '>= 0.1.0' if Gem.win_platform?
-gem "nokogiri", ">= 1.8.2"
+gem 'wdm', '>=0.1.0' if Gem.win_platform?
+gem "nokogiri", ">=1.8.2"
 gem "yajl-ruby", ">=1.3.1"
 gem "jekyll", ">=3.6.3"

_config.yml

@@ -12,7 +12,8 @@ color:
   secondary: f96b61
   secondary-dark: 333
 
-# Team names, titles and social links
+# Current lab members
+# Name, position and social links
 people:
 - name: Simon Garnier
   pic: simon
@@ -34,17 +35,19 @@ people:
     - title: link
       url: https://sites.google.com/site/jasonmgrahamus/
 
-- name: Lisa O'Bryan
-  pic: lisa
+- name: Michal Pluháček
+  pic: michal
   position: Postdoctoral Fellow
   social:
     - title: twitter
-      url: https://twitter.com/Project_Grunt
+      url: https://twitter.com/MPluhacek
 
 - name: Nicole Dykstra
   pic: nicole
   position: Graduate Student
   social:
+    - title: twitter
+      url: https://twitter.com/enephdee
     - title: linkedin
       url: https://www.linkedin.com/in/nicolefdykstra
 
@@ -85,54 +88,41 @@ people:
   pic: maggie
   position: Graduate Student
   social:
+    - title: twitter
+      url: https://twitter.com/GosiaVisniewska
     - title: linkedin
       url: https://www.linkedin.com/pub/maggie-wisniewska/44/858/515
 
-- name: Prit Zaveri
-  pic: prit
-  position: Master Student
-
-- name: Scott Bingham
-  pic: default
-  position: Undergraduate Student, MBI REU intern
-
-- name: Nicole Korzeniecki
+- name: Daniel Meza
   pic: default
-  position: Undergraduate Student, MBI REU intern
-
-- name: Wajihah Memon
-  pic: wajihah
   position: Undergraduate Student
 
-- name: Amisha Naik
-  pic: amisha
-  position: Undergraduate Student
-
-- name: Oluwatobi Olarogba
-  pic: default
-  position: Undergraduate Student, LSAMP intern
-
 - name: Ana Pais
   pic: default
   position: Undergraduate Student
 
-- name: Ezekiel Sandor
+- name: Saumil Parikh
   pic: default
-  position: Undergraduate Student, MBI REU intern
+  position: Undergraduate Student
 
 - name: Purva Shah
   pic: purva
   position: Undergraduate Student, Lab Assistant
 
-- name: Zainab Shahsamand
-  pic: default
-  position: Undergraduate Student
-
 - name: Matt Dreyer
   pic: default
   position: High School Student, Provost Summer Research Fellow
 
+# Former lab members
+# Name, position and social links
 people_old:
+- name: Lisa O'Bryan
+  pic: lisa
+  position: Postdoctoral Fellow
+  social:
+    - title: twitter
+      url: https://twitter.com/Project_Grunt
+
 - name: Chris Reid
   pic: chris
   position: Postdoctoral Fellow & Australian Extraordinaire
@@ -172,6 +162,10 @@ people_old:
   pic: oswaldo
   position: Master Student
 
+- name: Prit Zaveri
+  pic: prit
+  position: Master Student
+
 - name: Hala Abbas
   pic: default
   position: Undergraduate Student
@@ -188,6 +182,10 @@ people_old:
   pic: default
   position: Undergraduate Student
 
+- name: Scott Bingham
+  pic: default
+  position: Undergraduate Student, MBI REU intern
+
 - name: Archana Bottu
   pic: archana
   position: Undergraduate Student
@@ -244,6 +242,10 @@ people_old:
   pic: default
   position: Undergraduate Student
 
+- name: Nicole Korzeniecki
+  pic: default
+  position: Undergraduate Student, MBI REU intern
+
 - name: Jianna Kurian
   pic: default
   position: Undergraduate Student, Lab Assistant
@@ -264,10 +266,22 @@ people_old:
   pic: default
   position: Undergraduate Student
 
+- name: Wajihah Memon
+  pic: wajihah
+  position: Undergraduate Student
+
 - name: Matthew Moreno
   pic: default
   position: Undergraduate Student, MBI REU intern
 
+- name: Amisha Naik
+  pic: amisha
+  position: Undergraduate Student
+
+- name: Oluwatobi Olarogba
+  pic: default
+  position: Undergraduate Student, LSAMP intern
+
 - name: Ami Patel
   pic: default
   position: Undergraduate Student
@@ -292,6 +306,10 @@ people_old:
   pic: suraj
   position: Undergraduate Student
 
+- name: Ezekiel Sandor
+  pic: default
+  position: Undergraduate Student, MBI REU intern
+
 - name: Albert Saez
   pic: default
   position: Undergraduate Student
@@ -308,6 +326,10 @@ people_old:
   pic: default
   position: Undergraduate Student
 
+- name: Zainab Shahsamand
+  pic: default
+  position: Undergraduate Student
+
 - name: Balvir Singh
   pic: default
   position: Undergraduate Student

_includes/aboutus.html

@@ -46,7 +46,7 @@ <h4 class="service-heading">What is Swarm Intelligence?</h4>
                     </span>
                 <h4 class="service-heading">Latest news from the lab</h4>
                 <ul class="posts">
-                    {% for post in site.categories.blog limit:7 %}
+                    {% for post in site.categories.blog limit:5 %}
                     <li style="text-align: justify; font-size: 95%;">
                         <span>{{ post.date | date: "%b %-d, %Y" }}</span> &raquo;
                         <a href="{{ BASE_PATH }}{{ post.url }}">
@@ -59,4 +59,4 @@ <h4 class="service-heading">Latest news from the lab</h4>
             </div>
         </div>
     </div>
-</section>
+</section>

_posts/2019-03-01-data-model-2019.md

@@ -0,0 +1,17 @@
+---
+title: Announcing the 4th Collaborative Workshop on Modeling Collective Behavior
+date: 2019-03-01
+author: Simon Garnier
+layout: post
+type: post
+category:
+    - blog
+published: true
+
+---
+
+The SwarmLab is pleased to announce the 4th Collaborative Workshop on Modeling Collective Behavior, funded by the NSF OAC Public Access Initiative [grant #1838955](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1838955). The goal of this workshop is to provide researchers coming from mathematics, physics, engineering and biology with experience in working collaboratively to model and analyze data produced by research in collective behavior. This year we are also including an interdisciplinary art/science project (see Project 4 below) that will use virtual reality to explore and interact with data and models of collective behaviors.
+
+All information about the workshop, including application instructions and deadline, can be found [here](/meetings/data_model_2019/).
+
+![banner](/img/posts/data_model_2019/banner.png){: .full}

_posts/2019-03-09-new-publication.md

@@ -0,0 +1,17 @@
+---
+title: New publication - "Temporal and spatial pattern of trail clearing in the Australian meat ant, <i>Iridomyrmex purpureus</i>"
+date: 2019-03-09
+author: Simon Garnier
+layout: post
+type: post
+category:
+    - blog
+published: true
+
+---
+
+The SwarmLab is happy to announce the publication of: [Middleton, E. J. T., Garnier, S., Latty, T., and Reid, C. R. (2019). Temporal and spatial pattern of trail clearing in the Australian meat ant, *Iridomyrmex purpureus*. Anim. Behav. 150, 97–111. doi:10.1016/j.anbehav.2019.02.006](https://doi.org/10.1016/j.anbehav.2019.02.006)
+
+---
+
+**Abstract:** Many ant species use trails to connect important resources. In addition, some ants actively clear obstacles from their trails. Although trail clearing is thought to be beneficial in decreasing travel time, the physical process of clearing requires an investment of time and energy. Given that trail clearing is a decentralized process, how do colonies decide when to invest in clearing? In this study, we examined trail clearing in the Australian meat ant, using artificial semipermeable barriers mimicking grass. We tested the hypothesis that investment in clearing was influenced by the abundance and physical toughness of obstacles and that the selection of which grass blade to cut was a nonrandom process that decreases travel distance. We found that low abundance/low toughness treatments experienced the greatest amount of clearing and high abundance/high toughness the least. Although ants did not clear an optimally efficient trail, the results of our percolation analysis support the inference that the ants strategically deployed clearing, taking multiple factors into account when deciding to invest in this strategy. The resultant clearing patterns provided shorter travel routes for foraging ants than would be expected by the random removal of obstacles.

_posts/2019-03-24-new-publication.md

@@ -0,0 +1,19 @@
+---
+title: New publication - ""
+date: 2019-03-24
+author: Simon Garnier
+layout: post
+type: post
+category:
+    - blog
+published: false
+
+---
+
+The SwarmLab is happy to announce the publication of: [O’Bryan, L., Abaid, N., Nakayama, S., Dey, T., King, A., Cowlishaw, G., et al. (2019). Contact Calls Facilitate Group Contraction in Free-ranging Goats (Capra aegagrus hircus). Frontiers in Ecology and Evolution 7, 73. doi:10.3389/fevo.2019.00073](https://www.frontiersin.org/articles/10.3389/fevo.2019.00073/)
+
+---
+
+**Abstract:**
+
+Many social animal species produce vocalizations believed to facilitate group contraction when one or more group members have become distant. However, the mechanisms underlying this function remain unclear for many species. We examined this question with data on a semi-free ranging group of 16 adult domesticated goats (*Capra aegagrus hircus*) inhabiting Tsaobis Nature Park, Namibia. All goats wore dataloggers consisting of a GPS and audio recorder for 5-6 hours per day for 10 days, providing continuous data on their geolocations and vocal communication. We found that callers were farther from the group centroid than expected by chance and that call production was associated with the cessation of group expansion and subsequent group contraction. We did not find strong evidence for antiphonal call exchange between distant and core group members. Rather, we found that (i) call production by distant group members is associated with a significant reduction of group movement away from the caller, and (ii) call production by core group members is associated with greater, though not significantly greater, group movement towards the caller. These findings suggest that calls may be used by distant, and potentially core, group members to facilitate the contraction of group spread. Results from our study clarify the mechanisms through which social animals can regulate collective movement behavior and the specific role that vocalizations play in this process.

_posts/2019-03-25-new-publication.md

@@ -0,0 +1,21 @@
+---
+title: New publication - ""
+date: 2019-03-14
+author: Simon Garnier
+layout: post
+type: post
+category:
+    - blog
+published: false
+
+---
+
+The SwarmLab is happy to announce the publication of: [Ray, S., Valentini, G., Shah, P., Haque, A., Reid, C., Weber, G., et al. (2019). Information Transfer During Food Choice in the Slime Mold Physarum polycephalum. Frontiers in Ecology and Evolution 7, 67. doi:10.3389/fevo.2019.00067]](https://www.frontiersin.org/articles/10.3389/fevo.2019.00067/)
+
+This paper is a first publication for Subash, Purva and Abid. Many congratulations to them!
+
+---
+
+**Abstract:**
+
+Throughout evolution, living systems have developed mechanisms to make adaptive decisions in the face of complex and changing environmental conditions. Most organisms make such decisions despite lacking a neural architecture. This is the case of the acellular slime mold *Physarum polycephalum* that has demonstrated remarkable information processing and problem-solving abilities. Previous studies suggest that the membrane of *P. polycephalum* plays an important role in integrating and processing information leading to the selection of a resource to exploit. The cyclical contraction-relaxation pattern of the membrane changes with the local quality of the environment, and individual contractile regions within a *P. polycephalum* can entrain neighboring regions, providing a potential mechanism for information processing and propagation. In this study, we use an information-theoretic tool, transfer entropy, to study the flow of information in single tubule segments of *P. polycephalum* in a binary choice between two food sources. We test *P. polycephalum* tubules in two food choice conditions, where the two available options are either symmetric in their nutrient concentrations or with one more concentrated in nutrients than the other (i.e., asymmetric). We measure the contractile pattern of the *P. polycephalum* membrane and use these data to explore the direction and amount of information transfer along the tubule as a function of the cell’s final decision. We find that the direction of information transfer is different in the two experimental conditions, and the amount of information transferred is inversely proportional to the distance between different contractile regions. Our results show that regions playing a leading role in information transfer changes with the decision-making challenges faced by *P. polycephalum*.