Merge branch 'main' into collapse_abstracts

.github/workflows/jekyll.yml

@@ -108,6 +108,6 @@ jobs:
           sudo chmod 600 $SSH_KEY_PATH
           echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts
           wget https://raw.githubusercontent.com/UCSD-E4E/website2.0/main/_deploy_e4e-dev.sh
-          scp -i $SSH_KEY_PATH _deploy_e4e-dev.sh deploy@kastner-ml.dynamic.ucsd.edu:/tmp/deploy_e4e-dev.sh
-          ssh -i $SSH_KEY_PATH deploy@kastner-ml.dynamic.ucsd.edu '/bin/bash /tmp/deploy_e4e-dev.sh'
+          scp -i $SSH_KEY_PATH _deploy_e4e-dev.sh [email protected]:/tmp/deploy_e4e-dev.sh
+          ssh -i $SSH_KEY_PATH [email protected] '/bin/bash /tmp/deploy_e4e-dev.sh'
 

Gemfile.lock

@@ -105,7 +105,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rexml (3.3.7)
+    rexml (3.3.9)
     rouge (4.4.0)
     safe_yaml (1.0.5)
     sass-embedded (1.79.3-arm64-darwin)
@@ -124,7 +124,7 @@ GEM
       tzinfo (>= 1.0.0)
     unicode-display_width (2.6.0)
     wdm (0.1.1)
-    webrick (1.8.1)
+    webrick (1.8.2)
 
 PLATFORMS
   arm64-darwin-21

_bibliography/publications.bib

@@ -1,3 +1,23 @@
+@InProceedings{ayers_perry_prestrelski_etal_neurips_2024,
+  title={A Deep Learning Approach to the Automated Segmentation of Bird Vocalizations from Weakly Labeled Crowd-sourced Audio},
+  author={Ayers, Jacob and Perry, Sean and Prestrelski, Samantha and Zhang, Tianqi and von Schoenfeldt, Ludwig and Blue, Mugen and Steinberg, Gabriel and Tobler, Mathias and Ingram, Ian and Schurgers, Curt and Kastner, Ryan},
+  booktitle={NeurIPS 2024 Workshop on Tackling Climate Change with Machine Learning},
+  url={https://www.climatechange.ai/papers/neurips2024/8},
+  year={2024},
+  month=dec,
+  abstract={Ecologists interested in monitoring the effects caused by climate change are increasingly turning to passive acoustic monitoring, the practice of placing autonomous audio recording units in ecosystems to monitor species richness and occupancy via species calls. However, identifying species calls in large datasets by hand is an expensive task, leading to a reliance on machine learning models. Due to a lack of annotated datasets of soundscape recordings, these models are often trained on large databases of community created focal recordings. A challenge of training on such data is that clips are given a "weak label," a single label that represents the whole clip. This includes segments that only have background noise but are labeled as calls in the training data, reducing model performance. Heuristic methods exist to convert clip-level labels to "strong" call-specific labels, where the label tightly bounds the temporal length of the call and better identifies bird vocalizations. Our work improves on the current weakly to strongly labeled method used on the training data for BirdNET, the current most popular model for audio species classification. We utilize an existing RNN-CNN hybrid, resulting in a precision improvement of 12% (going to 90% precision) against our new strongly hand-labeled dataset of Peruvian bird species.},
+}
+
+@MastersThesis{Ayers2024,
+  title={An Exploration of Automated Methods for the Efficient Acquisition of Training Data for Acoustic Species Identification},
+  author={Ayers, Jacob Glenn},
+  year={2024},
+  month=jun,
+  school={University of California San Diego},
+  abstract={Passive acoustic monitoring is a field that strives to understand the health of ecosystems around the world through the acoustics of natural soundscapes. By identifying fauna vocalizations within soundscapes, we begin to build a quantitative understanding of local biodiversity populations, a key indicator of ecosystem health. The reduced cost of audio recorders have enabled researchers to collect datasets at a scale untenable in years past. These datasets are too vast for exhaustive human identification of species vocalizations. To which, researchers hope to train deep learning models for automated acoustic species identification to mitigate the burden of human labor.},
+  url={https://escholarship.org/content/qt3xk2377r/qt3xk2377r.pdf},
+}
+
 @Article{WallaceGurungKastner_JCGI_2024,
   author    = {Wallace, Ronan and Gurung, Yungdrung Tsewang and Kastner, Ryan},
   journal   = {Journal of Critical Global Issues},

_data/main_nav.yml

@@ -27,8 +27,12 @@ toc:
         url: /acoustic-species-identification
       - name: Mangrove Monitoring
         url: /mangrove-monitoring
+      - name: Maya Archeology
+        url: /maya-archaeology 
       - name: Smartfin
         url: /smartfin
+      - name: Aqua3D
+        url: /aqua3d
       - name: FishSense
         url: /fishsense
       - name: Floods of Lubra

_data/opportunities.yml

@@ -86,37 +86,49 @@
   - Have worked with NoSQL databases (MongoDB)
   - Experience with any testing frameworks
 - project: Radio Telemetry Tracker
-  title: Mechanical Engineer
+  title: User Interface Developer
   link: /radio-collar-tracker
-  description: The Radio Telemetry Tracking project seeks to aid scientists in the monitoring and conservation of wildlife by offering an efficient and reliable method of tracking animals. We are currently working on creating a long-term monitoring system that requires hardware mounts to be designed and built, and are seeking students with background in mechanical engineering to help us. We would be looking for students to commit at least 4 hours a week.
+  description: The Radio Telemetry Tracker project aims to develop an intuitive graphical user interface (GUI) that displays location estimates of transmitters and animals, provides status updates from field devices, and enables users to control these devices and access previous deployments. We are seeking enthusiastic students interested in designing and developing interfaces that are both functional and visually appealing.
   required:
-  - SolidWorks CAD + Drawings
-  - 3D Printing and/or Laser Cutting
-  - Familiarity with using hand tools (screwdriveres, wrenches, etc)
+  - Python
+  - HTML/CSS/JavaScript
+  - Git/GitHub
+  desired:
+  - Experience with Flask
+  - UI/UX design experience
+  - Experience with React
+  - Experience with GIS-based mapping libraries/tools (Leaflet, Folium, QGIS, etc.)
 - project: Radio Telemetry Tracker
-  title: Electrical Engineer
+  title: Embedded Systems Engineer
   link: /radio-collar-tracker
-  description: The Radio Telemetry Tracking project seeks to aid scientists in the monitoring and conservation of wildlife by offering an efficient and reliable method of tracking animals. We are looking for students to help maintain, develop, and test next generation monitoring systems ranging from drone payload trackers to mobile tracking stations. We would be looking for students to commit at least 4 hours a week.
+  description: The Radio Telemetry Tracker project aims to provide system prototypes to collaborators for field testing. We are seeking students to develop reliable control systems for our field devices. This role involves selecting appropriate components, assembling the devices, and creating software that enables wireless communication between the system's peripheral devices and the user interface.
   required:
-  - Circuit design
-  - Experience in electrical debugging
-  - Technical documentation
+  - Basic communication interfaces (I2C, Serial, GPIO, etc.)
+  - Python, C++, or Rust programming
+  - Experience with microcontrollers/microprocessors (Arduino, Raspberry Pi, etc.)
   desired:
-  - Experience soldering
+  - Experience with IoT, particularly long-range communication
+  - Experience with solar panels and battery management
 - project: Radio Telemetry Tracker
-  title: Student Co-Lead
+  title: Mechanical Engineer
   link: /radio-collar-tracker
-  description: |
-    Engineers for Exploration (E4E) is looking for motivated students to take on a leadership role for our Radio Telemetry Tracker (RTT) team. This role could tie into an undergraduate or master's thesis project, and we encourage students to explore this option. RTT is a multidisciplinary systems project in collaboration with the San Diego Zoo Wildlife Alliance which aims to improve methods of tracking animals using radio telemetry. This type of animal tracking picks up signals from radio transmitters which have been attached to or embedded in subject animals. Traditional on-foot methods of radio telemetry require researchers to trek through difficult terrain with unwieldy antennae, so we're developing two systems to make the process easier: a drone-based system to fly over the terrain, and a tower-based system to be set up and left to collect data with little supervision.
-
-    We have deployed our system to the field previously, and the project's current goals include designing a new PCB for our payload, redesigning our payload's physical housing, and developing software to communicate with the system's peripheral devices, all to prepare for upcoming deployments. Examples of skills which would be helpful for this role include systems engineering, PCB design, electrical debugging, embedded programming, and digital signal processing.
-
-    We assemble our system with custom sensors to gather the data we need and record it for later analysis. Due to such customization and the multidisciplinary nature of RTT, this project has many moving parts, and the ideal candidate would have some experience navigating such problems of complexity. This role includes the expectation and opportunity to deploy the system you develop into the field in order to track animals and report on results.
+  description: To prepare for a field test of our system, the Radio Telemetry Tracker team needs to develop durable mounts and enclosures for field devices that will be deployed on drones and towers for extended periods. We are seeking students to help design and construct these mounts and enclosures.
+  required:
+  - CAD Design + Drafting
+  - SolidWorks or similar CAD software
+  - 3D Printing 
+  desired:
+  - Designing with IP and IP protection in mind
+  - Experience with hand tools
+- project: Radio Telemetry Tracker
+  title: Digital Signal Processing Researcher
+  link: /radio-collar-tracker
+  description: The Radio Telemetry Tracker team is seeking students to help research and develop digital signal processing and location estimation algorithms. This role focuses on the core research aspects of the project. We are looking for students to design methods for processing raw data from software-defined radios (SDR) and converting it into accurate transmitter location estimates.
+  required:
+  - Reading research papers
+  - Basic DSP knowledge (signal basics, modulation/demodulation, frequency domain analysis, etc.)
+  - MATLAB, Python, C++, or Rust programming
   desired:
-  - Leadership/Project Management
-  - PCB Design/Layout/Assembly/Testing
-  - Mechanical Design/Fabrication/Assembly/Testing
-  - Digital Interfacing (I2C/Serial)
-  - Embedded Linux (I2C/Serial/GPIO/sysfs/networking)
-  - Python (pybind11/threading)
-  - Digital Signal Processing (STFT/spectral analysis/mixing)
+  - Writing research papers
+  - Antenna design
+  - Tangible experience with SDRs (USRP, HackRF, Airspy)

_data/people.yml

@@ -970,12 +970,13 @@
   start: 2020
   end: 2020
 
-- description: Baboons on the Move since 2018, FishSense since 2022
+- description: Baboons on the Move since 2018, FishSense since 2022, Aqua3D since 2024
   expedition: true
   image: assets/people/c.crutchfield.jpg
   level: Project Lead
   name: Christopher Crutchfield
   start: 2018
+  link: https://ccrutchf.github.io/
 - description: Baboons on the Move 2018-2023
   expedition: false
   image: assets/people/a.ngo.jpg

_includes/head.html

@@ -1,11 +1,4 @@
 <head>
-  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.7.1/jquery.min.js"></script>
-  <script src="{{ "/cache/foundation.min.js" | absolute_url }}"></script>
-  <script>
-    $(document).ready(function(){
-        $(document).foundation();
-    });
-  </script>
   <meta charset="utf-8">
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
@@ -14,18 +7,6 @@
   {%- endif -%}
   {%- seo -%}
 
-  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.7.1/jquery.min.js"></script>
-  <script src="{{ "/cache/foundation.min.js" | absolute_url }}"></script>
-  <!-- https://stackoverflow.com/questions/73978467/jekyll-datatables-below-sidebar -->
-  {%- if page.datatable == true -%}
-  <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.12.1/css/jquery.dataTables.css"> <!--add style sheet-->
-  <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.12.1/js/jquery.dataTables.js"></script> <!--add dataTables-->
-  <script>
-      $(document).ready( function () {
-      $('table.datatable').DataTable();
-      } );
-  </script>
-  {% endif %}
   <link rel="stylesheet" href="{{ "/cache/foundation.min.css" | absolute_url }}">
   <link rel="stylesheet" href="{{ "/assets/main.css" | absolute_url }}">
   <link rel="apple-touch-icon" sizes="180x180" href={{"/assets/apple-touch-icon.png" | absolute_url}}>

_layouts/archive.html

@@ -18,11 +18,13 @@ <h3 class="archive-post-title archive-post-link">{{ post.title }}</h3>
                     <img 
                         src="{{ post.featuredImage | string |  crop: '3:2+0+0,Center' | resize: '300x200' | format: 'webp' | absolute_url }}"
                         class="inline_image archive-image"
+                        alt="{{ post.featuredImageAlt | default: 'featured image' }}"
                     >
                     {% else %}
                     <img 
                         src="{{ 'e4e_website-no-e4e.png' |  crop: '3:2+0+0,Center' | resize: '300x200' | format: 'webp' | absolute_url }}"
                         class="inline_image archive-image"
+                        alt="E4E Logo, post has no featured image"
                     >
                     {% endif %}
 

_layouts/blog-post.html

@@ -16,7 +16,15 @@ <h1 class="post-title p-name" itemprop="name headline">{{ page.title | escape }}
   </header>
 
   <div class="featured-post-image">
-    <img alt="featured-image" width="816" height="auto" src="{{ page.featuredImage | relative_url }}" class="attachment-post-thumbnail size-post-thumbnail wp-post-thumbnail" sizes="(max-width: 816px) 100vw, 816px" >
+    <!-- we do allow for no images to be shown, could lead to bugs here... -->
+    <img 
+      alt="{{ page.featuredImageAlt | default: 'featured image' }}" 
+      width="816" 
+      height="auto" 
+      src="{{ page.featuredImage | relative_url }}" 
+      class="attachment-post-thumbnail size-post-thumbnail wp-post-thumbnail" 
+      sizes="(max-width: 816px) 100vw, 816px" >
+
   </div>
 
   <div class="post-content e-content" itemprop="articleBody">

_layouts/default.html

@@ -15,6 +15,18 @@
 
     {%- include footer.html -%}
 
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.7.1/jquery.min.js"></script>
+    <script src="{{ "/cache/foundation.min.js" | absolute_url }}"></script>
+    <!-- https://stackoverflow.com/questions/73978467/jekyll-datatables-below-sidebar -->
+    {%- if page.datatable == true -%}
+    <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.12.1/css/jquery.dataTables.css"> <!--add style sheet-->
+    <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.12.1/js/jquery.dataTables.js"></script> <!--add dataTables-->
+    <script>
+        $(document).ready( function () {
+        $('table.datatable').DataTable();
+        } );
+    </script>
+    {% endif %}
   </body>
 
 </html>

_layouts/home.html

@@ -23,7 +23,7 @@ <h2 class="home_header">EXPLORATION THROUGH TECHNOLOGY</h2>
       <a class="interesting_link" href="/welcome" style="font-weight: bold;">Interested in joining?</a>
       <br/>
       <br/>
-      <h2 class="home_header">SPONSER OUR RESERACH</h2>
+      <h2 class="home_header">SPONSOR OUR RESERACH</h2>
       <p>
         Your support allows us to involve more students, which allows us to continue our research on existing and future projects. It is easy and even a small amount can make a big impact.
         <a class="interesting_link" href="https://giveto.ucsd.edu/giving/home/gift-referral/a4b5012d-f622-42bd-947c-b977bf9466a7">
@@ -45,11 +45,13 @@ <h2 class="home_header">SPONSER OUR RESERACH</h2>
                 {%- if post.featuredImage -%}
                 <img 
                   src="{{ post.featuredImage | string |  crop: '3:2+0+0,Center' | resize: '300x200!' | format: 'webp' | absolute_url }}"
-                >
+                  alt="{{ post.featuredImageAlt | default: 'featured image' }}"
+                  >
                 {% else %}
                 <img 
                   src="{{ 'e4e_website-no-e4e.png' |  crop: '3:2+0+0,Center' | resize: '300x200' | format: 'webp' | absolute_url }}"
-                >
+                  alt="E4E Logo, post has no featured image"
+                  >
                 {% endif %}
               </div>
 

_posts/2013-04-01-test-post.md

@@ -2,6 +2,7 @@
 date: 2013-04-01 05:36:54+00:00
 description: null
 featuredImage: /assets/2013-04-01-test-post_E4ELogo.gif
+featuredImageAlt: Logo of E4E and test for alt system! 
 layout: blog-post
 slug: /test-post
 title: New Website!

_posts/2021-09-24-2021-fall-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2021-09-24 02:34:27+00:00
 description: null
-featuredImage: assets/2021-09-24-fa24-projects.png
+featuredImage: assets/recruiting/2021-09-24-fa24-projects.png
 layout: blog-post
 slug: /2021-fall-info-session
 title: 2021 Fall Info Session

_posts/2022-01-11-winter-2022-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2022-01-11 03:42:22+00:00
 description: null
-featuredImage: assets/2022-01-10-info-session.png
+featuredImage: assets/recruiting/2022-01-10-info-session.png
 layout: blog-post
 slug: /winter-2022-info-session
 title: Winter 2022 Info Session

_posts/2022-03-31-spring-2022-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2022-03-31 00:23:30+00:00
 description: null
-featuredImage: assets/2022-03-31-info-session.png
+featuredImage: assets/recruiting/2022-03-31-info-session.png
 author: Christopher Crutchfield
 layout: blog-post
 slug: /spring-2022-info-session

_posts/2022-09-30-fall-2022-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2022-09-30 02:23:07+00:00
 description: null
-featuredImage: assets/2022-09-30-info-session.png
+featuredImage: assets/recruiting/2022-09-30-info-session.png
 author: Nathan
 layout: blog-post
 slug: /fall-2022-info-session

_posts/2022-11-30-summer-reu.md

@@ -1,7 +1,7 @@
 ---
 date: 2022-11-30 04:17:40+00:00
 description: null
-featuredImage: assets/2022-11-29-2023-reu-recruitment.png
+featuredImage: assets/recruiting/2022-11-29-2023-reu-recruitment.png
 layout: blog-post
 slug: /engineers-for-exploration-e4e-summer-research-program-at-uc-san-diego-application-submission-by-february-15th-2023
 title: Engineers for Exploration (E4E) Summer Research Program at UC San Diego ­-

_posts/2023-01-13-winter-2023-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2023-01-13 03:06:15+00:00
 description: null
-featuredImage: assets/2023-01-12-info-session.png
+featuredImage: assets/recruiting/2023-01-12-info-session.png
 layout: blog-post
 slug: /winter-2023-info-session
 title: Winter 2023 Info Session

_posts/2023-04-04-spring-2023-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2023-04-04 06:05:55+00:00
 description: null
-featuredImage: assets/2023-04-03-info-session.png
+featuredImage: assets/recruiting/2023-04-03-info-session.png
 layout: blog-post
 slug: /spring-2023-info-session
 title: Spring 2023 Info Session

_posts/2023-09-30-fall-2023-info-session.md

@@ -1,6 +1,6 @@
 ---
 date: 2023-09-30 00:10:28+00:00
-featuredImage: assets/2023-09-29-info-session.png
+featuredImage: assets/recruiting/2023-09-29-info-session.png
 author: Tyler Flar
 layout: blog-post
 slug: /fall-2023-info-session

_posts/2024-04-03-spring-2024-info-session.md

@@ -1,7 +1,7 @@
 ---
 date: 2024-04-03 00:00:00-07:00
 author: Nathan
-featuredImage: assets/2024-04-03-info-session.png
+featuredImage: assets/recruiting/2024-04-03-info-session.png
 layout: blog-post
 slug: /spring-2024-info-session
 title: Spring 2024 Info Session