diff --git a/config/_default/menus.toml b/config/_default/menus.toml index 67899ba4965..6186af0b882 100644 --- a/config/_default/menus.toml +++ b/config/_default/menus.toml @@ -8,50 +8,40 @@ url = "#about" weight = 10 -[[main]] - name = "Values" - url = "#values" - weight = 15 - [[main]] name = "People" url = "#people" weight = 20 -[[main]] - name = "Positions" - url = "#positions" - weight = 30 - -[[main]] - name = "Posts" - url = "#posts" - weight = 35 - [[main]] name = "Projects" url = "#projects" weight = 40 [[main]] - name = "Talks" - url = "#talks" + name = "Presentations" + url = "#presentations" weight = 50 -[[main]] - name = "Software" - url = "#software" - weight = 60 - [[main]] name = "Publications" url = "#publications" weight = 70 +[[main]] + name = "Group resources" + url = "#group" + weight = 80 + +[[main]] + name = "Posts" + url = "#posts" + weight = 90 + [[main]] name = "Contact" url = "#contact" - weight = 80 + weight = 1000 # Link to a PDF of your resume/CV from the menu. # To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. diff --git a/content/authors/adkris/_index.md b/content/authors/adkris/_index.md index bc5bceb7964..d6de23bd63a 100644 --- a/content/authors/adkris/_index.md +++ b/content/authors/adkris/_index.md @@ -12,7 +12,7 @@ weight: 30 superuser: false # Role/position -role: Undergraduate Research Assistant +role: Graduate Student # Organizations/Affiliations organizations: diff --git a/content/authors/ctuguina/_index.md b/content/authors/ctuguina/_index.md index 673ec3ebbd6..7d39eb583b6 100644 --- a/content/authors/ctuguina/_index.md +++ b/content/authors/ctuguina/_index.md @@ -12,7 +12,7 @@ weight: 30 superuser: false # Role/position -role: Research Assistant +role: Graduate Student # Organizations/Affiliations organizations: diff --git a/content/position/2021-06-30-postdoc-hake-ml/index.md b/content/group/2021-06-30-postdoc-hake-ml/index.md similarity index 100% rename from content/position/2021-06-30-postdoc-hake-ml/index.md rename to content/group/2021-06-30-postdoc-hake-ml/index.md diff --git a/content/position/2021-09-06-rse/index.md b/content/group/2021-09-06-rse/index.md similarity index 100% rename from content/position/2021-09-06-rse/index.md rename to content/group/2021-09-06-rse/index.md diff --git a/content/position/2021-12-04-cicoes-postdoc/index.md b/content/group/2021-12-04-cicoes-postdoc/index.md similarity index 100% rename from content/position/2021-12-04-cicoes-postdoc/index.md rename to content/group/2021-12-04-cicoes-postdoc/index.md diff --git a/content/position/2022-08-22-postdoc-hake-ml/index.md b/content/group/2022-08-22-postdoc-hake-ml/index.md similarity index 99% rename from content/position/2022-08-22-postdoc-hake-ml/index.md rename to content/group/2022-08-22-postdoc-hake-ml/index.md index 53234b13114..915b9d92ee6 100644 --- a/content/position/2022-08-22-postdoc-hake-ml/index.md +++ b/content/group/2022-08-22-postdoc-hake-ml/index.md @@ -6,7 +6,7 @@ authors: - leewj - vms16 slug: 2022-08-22-postdoc -draft: false +draft: true tags: summary: " " diff --git a/content/position/_index.md b/content/group/_index.md similarity index 83% rename from content/position/_index.md rename to content/group/_index.md index c6016475b42..da8f0a27be1 100644 --- a/content/position/_index.md +++ b/content/group/_index.md @@ -1,11 +1,11 @@ --- -title: Positions +title: Group resources # View. # 1 = List # 2 = Compact # 3 = Card -view: 3 +view: 2 # Optional header image (relative to `static/img/` folder). header: diff --git a/content/values/coc/coc_202203.md b/content/group/coc/coc_202203.md similarity index 98% rename from content/values/coc/coc_202203.md rename to content/group/coc/coc_202203.md index 4f95ec13461..a5978b1c792 100644 --- a/content/values/coc/coc_202203.md +++ b/content/group/coc/coc_202203.md @@ -1,7 +1,7 @@ --- # Documentation: https://sourcethemes.com/academic/docs/managing-content/ title: "Code of Conduct & What we value" -date: 2022-03-29T00:00:00-08:00 +date: 2022-03-29 authors: slug: 2022-03-coc-values draft: false diff --git a/content/values/coc/index.md b/content/group/coc/index.md similarity index 83% rename from content/values/coc/index.md rename to content/group/coc/index.md index 5d51dfbab04..89fb5a57260 100644 --- a/content/values/coc/index.md +++ b/content/group/coc/index.md @@ -1,9 +1,10 @@ --- # Documentation: https://sourcethemes.com/academic/docs/managing-content/ title: "Code of Conduct & What we value" -date: 2023-10-03T00:00:00-08:00 +date: 2024-09-29 authors: -slug: 2023-10-coc-values +slug: coc +weight: 10 draft: false tags: summary: "We review and discuss the code of conduct and what we value as a group regularly, as reminder and inspiration for ourselves." @@ -66,3 +67,12 @@ Echospace is dedicated to providing a harassment-free experience for everyone, r - Enable and encourage growth by everyone in the group, in directions that align with what they’re interested in - Be comfortable bringing up issues or obstacles that hold you back from getting work done + +## Feedback Sharing + +Provide feedback on what to improve either in person or use the [Echospace Anonymous Feedback Form](https://forms.gle/NZFZBQLk9BoMLZCV6) if you prefer to remain anonymous. The form requires one to be logged with their `uw` email address, but we will not have access to it. + + +## Conflict Resolution + +If you see something inappropriate, let Wu-Jung or Valentina know immediately, or contact the [Office of the Ombud](https://www.washington.edu/ombud/) for support in conflict resolution. You can refer to some additional resources from the UW HR office [here](https://hr.uw.edu/policies/complaint-resolution/) or refer to your department for advice. diff --git a/content/group/communication/index.md b/content/group/communication/index.md new file mode 100644 index 00000000000..7ad4c6de8d9 --- /dev/null +++ b/content/group/communication/index.md @@ -0,0 +1,57 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "Communication within group" +# date: 2023-09-19 +authors: +slug: communication +weight: 40 +draft: false +show_date: false +tags: +summary: "Our current practice to communicate with each other in Echospace" + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +# Communication + +We use various modes of communication in Echospace to keep ourselves up-to-date on what we are each working on and coordinate. + +Depending on who's involved and the context, we use different methods to communicate. In general: +- Internal (among group members): mostly Slack +- External (with colleagues outside of the group): emails +- GitHub: PR and issues, see [here](./compute-git.md) for how to get started +- Talking: we do talk in analog form! + +In terms of expectations: +- We encourage proactive and frequent communication; for most projects we meet at least weekly to keep each other updated and set short and long term goals +- Immediate response are not expected unless urgent +- People may send messages/emails at their convenient time; aim to respond within a reasonable time frame +- Phone/text: usually reserved for urgent communication or offsite coordination +- Ask us/everyone for help, and provide help if you can! + + +## Slack workspace +- Default channels you're added to: + - #general + - #help + - #random +- Feel free to: + - Add or remove yourself from channels, but make sure you stay in the know for your projects, as well as group announcements + - Create new channels and announce in the #general channel for others to join \ No newline at end of file diff --git a/content/group/compute_docs/index.md b/content/group/compute_docs/index.md new file mode 100644 index 00000000000..1ff256d5cd8 --- /dev/null +++ b/content/group/compute_docs/index.md @@ -0,0 +1,38 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "Computing startup resources" +date: 2023-12-07 +authors: +slug: compute_docs +weight: 30 +draft: false +tags: +summary: "Useful starting computing resources" + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +In this collection we share useful starting computing resources among echospace group members. + +- [Conda and Jupyter](https://echospace-group-docs.readthedocs.io/en/latest/compute-conda-jupyter.html) +- [Git and GitHub](https://echospace-group-docs.readthedocs.io/en/latest/compute-git.html) +- [Cloud computing](https://echospace-group-docs.readthedocs.io/en/latest/compute-cloud.html) +- [HPC and SLURM](https://echospace-group-docs.readthedocs.io/en/latest/compute-hpc.html) +- [OSN data access](https://echospace-group-docs.readthedocs.io/en/latest/compute-osn.html) +- [Other topics to be covered](https://echospace-group-docs.readthedocs.io/en/latest/compute-others.html) \ No newline at end of file diff --git a/content/position/opportunities/index.md b/content/group/opportunities/index.md similarity index 72% rename from content/position/opportunities/index.md rename to content/group/opportunities/index.md index 9816db5e5cc..5f458a3ff4c 100644 --- a/content/position/opportunities/index.md +++ b/content/group/opportunities/index.md @@ -1,15 +1,12 @@ --- # Documentation: https://sourcethemes.com/academic/docs/managing-content/ title: "Opportunities at Echospace" -date: 2022-07-25T00:00:00-08:00 -authors: - - leewj - - vms16 - - emiliom -slug: fellowships +date: 2024-09-01 +slug: opportunities +weight: 20 draft: false tags: -summary: " " +summary: "Interested in joining Echospace? Check out the latest info here!" # Customize share: false @@ -32,13 +29,14 @@ image: ## General information -We welcome researchers and students with diverse backgrounds to come work with us in Echospace! If you are interested but do not find a specific position posted, feel free to reach out to us directly. Please include a cover letter and a CV/resume when initiating the contact, so that we have a better idea what you are looking for. +We welcome researchers and students with diverse backgrounds to come work with us in Echospace! If you don't see a specific position below, feel free to reach out to us directly. Please include a cover letter and a CV/resume when initiating the contact, so that we have a better idea what you are looking for and your background. ## Fellowship opportunities Below is a list of fellowship opportunities within and outside of UW. Relevant areas include but are not limited to fisheries and ocean acoustics, animal echolocation (bats and dolphins), marine ecology, and environmental data science. Feel free to reach out to us for questions and discussion. + ### Postdoc fellowships #### University of Washington @@ -49,7 +47,7 @@ Below is a list of fellowship opportunities within and outside of UW. Relevant a #### External - [NSF Ocean Sciences (OCE) Postdoctoral Research Fellowships (OCE-PRF)](https://beta.nsf.gov/funding/opportunities/ocean-sciences-postdoctoral-research-fellowships-oce-prf-0) - [NSF Division of Earth Sciences (EAR) Postdoctoral Fellowships (EAR-PF)](https://beta.nsf.gov/funding/opportunities/ear-postdoctoral-fellowships-ear-pf) -- [Acoustical Society of America (ASA) Hunt Postdoctoral Research fellowship](https://acousticalsociety.org/fellowships-and-scholarships/) +- [Acoustical Society of America (ASA) F. V. Hunt Postdoctoral Research fellowship](https://acousticalsociety.org/fellowships-and-scholarships/) ### Graduate fellowships @@ -59,4 +57,5 @@ Below is a list of fellowship opportunities within and outside of UW. Relevant a ### Undergraduate fellowships -- [Mary Gates Research Scholarship](https://expd.uw.edu/mge/apply/research/) +- [UW Mary Gates Research Scholarship](https://expd.uw.edu/mge/apply/research/) +- [APL DINO-SIP Diverse + Inclusive Naval Oceanographic Summer Intership Program](https://www.apl.uw.edu/education/dino_sip.php) diff --git a/content/home/contact.md b/content/home/contact.md index 1e0dba97ae2..3d02f4e686f 100644 --- a/content/home/contact.md +++ b/content/home/contact.md @@ -3,7 +3,7 @@ widget = "contact" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. active = true # Activate this widget? true/false -weight = 80 # Order that this section will appear. +weight = 1000 # Order that this section will appear. title = "Contact" subtitle = "" @@ -17,4 +17,3 @@ autolink = true # 2: formspree.io email_form = 0 +++ - diff --git a/content/home/software.md b/content/home/group.md similarity index 92% rename from content/home/software.md rename to content/home/group.md index 49c0eafb5bc..f13461f543e 100644 --- a/content/home/software.md +++ b/content/home/group.md @@ -3,32 +3,32 @@ widget = "portfolio" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. active = true # Activate this widget? true/false -weight = 60 # Order that this section will appear. +weight = 80 # Order that this section will appear. -title = "Software" +title = "Group resources" subtitle = "" [content] # Page type to display. E.g. project. - page_type = "software" - + page_type = "group" + # Filter toolbar (optional). # Add or remove as many filters (`[[content.filter_button]]` instances) as you like. # To show all items, set `tag` to "*". # To filter by a specific tag, set `tag` to an existing tag name. # To remove toolbar, delete/comment all instances of `[[content.filter_button]]` below. - + # Default filter index (e.g. 0 corresponds to the first `[[filter_button]]` instance below). filter_default = 0 - + # [[content.filter_button]] # name = "All" # tag = "*" - + # [[content.filter_button]] # name = "Deep Learning" # tag = "Deep Learning" - + # [[content.filter_button]] # name = "Other" # tag = "Demo" @@ -42,7 +42,7 @@ subtitle = "" # 2 = Compact # 3 = Card # 5 = Showcase - view = 3 + view = 2 # For Showcase view, flip alternate rows? flip_alt_rows = false @@ -52,25 +52,25 @@ subtitle = "" # Uncomment (by removing `#`) an option to apply it. # Choose a light or dark text color by setting `text_color_light`. # Any HTML color name or Hex value is valid. - + # Background color. # color = "navy" - + # Background gradient. # gradient_start = "DeepSkyBlue" # gradient_end = "SkyBlue" - + # Background image. # image = "background.jpg" # Name of image in `static/img/`. # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. # Text color (true=light or false=dark). # text_color_light = true - + [advanced] - # Custom CSS. + # Custom CSS. css_style = "" - + # CSS class. css_class = "" +++ diff --git a/content/home/posts.md b/content/home/posts.md index 5eb1307e175..07a6c13034a 100644 --- a/content/home/posts.md +++ b/content/home/posts.md @@ -5,9 +5,9 @@ widget = "pages" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. active = true # Activate this widget? true/false -weight = 35 # Order that this section will appear. +weight = 80 # Order that this section will appear. -title = "Recent Posts" +title = "Posts" subtitle = "" [content] diff --git a/content/home/talks.md b/content/home/presentations.md similarity index 98% rename from content/home/talks.md rename to content/home/presentations.md index ad8c5eaa4e2..068c46d1d60 100644 --- a/content/home/talks.md +++ b/content/home/presentations.md @@ -7,7 +7,7 @@ headless = true # This file represents a page section. active = true # Activate this widget? true/false weight = 50 # Order that this section will appear. -title = "Recent & Upcoming Talks" +title = "Presentations" subtitle = "" [content] diff --git a/content/home/publications.md b/content/home/publications.md index 23e378cf2e8..2018364d022 100644 --- a/content/home/publications.md +++ b/content/home/publications.md @@ -7,7 +7,7 @@ headless = true # This file represents a page section. active = true # Activate this widget? true/false weight = 70 # Order that this section will appear. -title = "Recent Publications" +title = "Publications" subtitle = "" [content] @@ -66,5 +66,3 @@ subtitle = "" # CSS class. css_class = "" +++ - - diff --git a/content/home/values.md b/content/home/values.md deleted file mode 100644 index ef01a8d32f9..00000000000 --- a/content/home/values.md +++ /dev/null @@ -1,68 +0,0 @@ -+++ -# A Recent Blog Posts section created with the Pages widget. -# This section displays recent blog posts from `content/post/`. - -widget = "pages" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = true # Activate this widget? true/false -weight = 15 # Order that this section will appear. - -title = "What we value" -subtitle = "" - -[content] - # Page type to display. E.g. post, talk, or publication. - page_type = "values" - - # Choose how much pages you would like to display (0 = all pages) - count = 5 - - # Choose how many pages you would like to offset by - offset = 0 - - # Page order. Descending (desc) or ascending (asc) date. - order = "desc" - - # Filter posts by a taxonomy term. - [content.filters] - tag = "" - category = "" - publication_type = "" - author = "" - exclude_featured = false - -[design] - # Toggle between the various page layout types. - # 1 = List - # 2 = Compact - # 3 = Card - # 4 = Citation (publication only) - view = 2 - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "navy" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "background.jpg" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - - # Text color (true=light or false=dark). - # text_color_light = true - -[advanced] - # Custom CSS. - css_style = "" - - # CSS class. - css_class = "" -+++ diff --git a/content/project/2018-muri-echolocation/index.md b/content/project/2018-muri-echolocation/index.md deleted file mode 100644 index 33a7bcbf835..00000000000 --- a/content/project/2018-muri-echolocation/index.md +++ /dev/null @@ -1,35 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ -title: "Modeling target search by echolocating toothed whales" -date: 2018-01-01T14:50:00-08:00 -authors: -slug: 2018-muri-echolocation -weight: 40 -draft: false -tags: - - animal echolocation - - toothed whales -summary: "Modeling the echolocation-based target search behavior of toothed whales as an information-seeking process." - -# Customize -share: false -markup: md -math: true -featured: false - -# Featured image -# To use, place an image named `featured.jpg/png` in your page's folder. -# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width -# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight -# Set `preview_only` to `true` to just use the image for thumbnails. -image: - caption: - Placement options: 1 - focal_point: "Center" - preview_only: true - ---- - -Echolocating animals effortlessly navigate, hunt, and interact with their environment, despite cluttered and noisy return signals. Blind expert human echolocators prove that this capacity does not depend exclusively on biological specializations unique to particular species. This project is an integrated component of a larger collaborative project (see funding below) focused on active sensing in echolocating marine mammals and humans. The overarching goal of the interdisciplinary team is to use both toothed whales (odontocetes) and humans as model systems to identify the neural mechanisms that extract echo-acoustic information and the brain networks that build robust, invariant representations of auditory objects in complex auditory scenes. The UW-APL component of the project involves modeling the echolocation-based target search by toothed whales as an information-seeking behavior by extending the _infotaxis_ algorithm originally formulated in moth odor tracking problems into an _active sensing_ context. In parallel with the theoretical work, we also conducted an echolocation target discrimination experiment with a harbor porpoise to guide further model development. - -**Funding agency**: Office of Naval Research -- Multidisciplinary University Research Initiative (MURI) \ No newline at end of file diff --git a/content/software/echo-stat-tutorial/featured.png b/content/project/echo-stat-tutorial/featured.png similarity index 100% rename from content/software/echo-stat-tutorial/featured.png rename to content/project/echo-stat-tutorial/featured.png diff --git a/content/software/echo-stat-tutorial/index.md b/content/project/echo-stat-tutorial/index.md similarity index 100% rename from content/software/echo-stat-tutorial/index.md rename to content/project/echo-stat-tutorial/index.md diff --git a/content/project/echolocation_comsol/index.md b/content/project/echolocation_comsol/index.md new file mode 100644 index 00000000000..bef0cd0ba2a --- /dev/null +++ b/content/project/echolocation_comsol/index.md @@ -0,0 +1,39 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "Modeling sound propagation in the head of toothed whales" +date: 2022-07-01 +authors: +slug: echolocation-comsol +weight: 40 +draft: false +tags: + - echolocation + - finite element modeling +summary: "Understanding the interaction of sound with biological structures in toothed whale head." + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +Toothed whales, including species such as porpoises, dolphins, orca, and sperm whale, possess highly specialized anatomical structures in the head to support their biosonar systems - echolocation - through millions of years of evoluation. These animals have the remarkable ability to detect and track small targets over long distance and discriminate between minute differences between targets using echolocation, with performance often surpassing that of current human-made sonar systems. However, many questions remain in how exactly the unusual anatomical structures in the head of toothed whales are orchestrated to support such performance. + +As part of a Multidisciplinary University Research Initiative (MURI) project, we use finite element modeling techniques in combination with volumetric representations derived from computed tomography (CT) scans to predict the head-related transfer functions (HRTFs) of a dolphin head. The HRTFs summarizes the influence of the head to sounds propagating to the ears. We use HRTFs as a biologically meaningful proxy to provide a physics-based mechanistic understanding of the sound transduction processes. + + + +**Funding**: Office of Naval Research, Multidisciplinary University Research Initiative (MURI) program \ No newline at end of file diff --git a/content/project/echolocation_search/index.md b/content/project/echolocation_search/index.md new file mode 100644 index 00000000000..5ac9ba85eb0 --- /dev/null +++ b/content/project/echolocation_search/index.md @@ -0,0 +1,41 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "Target search and discrimination by echolocating toothed whales" +date: 2018 +authors: +slug: echolocation-search +weight: 40 +draft: false +tags: + - echolocation + - infotaxis +summary: "Modeling and analyzing the echolocation behavior of toothed whales." + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +Echolocating animals effortlessly navigate, hunt, and interact with their environment, despite cluttered and noisy return signals. Blind expert human echolocators prove that this capacity does not depend exclusively on biological specializations unique to particular species. This project is an integrated component of a larger collaborative Multidisciplinary University Research Initiative (MURI) project focused on active sensing in echolocating marine mammals and humans. The MURI team use both toothed whales (odontocetes) and humans as model systems to identify the neural mechanisms that extract echo-acoustic information and the brain networks that build and learn robust, invariant representations of auditory objects in complex auditory scenes. + +In Echospace, we undertake two interconnected components of this project: +- Model the echolocation-based target search by toothed whales as an information-seeking behavior by extending the _infotaxis_ algorithm originally formulated in moth odor tracking problems into an _active sensing_ context + +- Conduct and analyze the coupled acoustic sampling and movement behaviors of an echolocating harbor porpoise in a target discrimination experiment + + +**Funding agency**: Office of Naval Research, Multidisciplinary University Research Initiative (MURI) program \ No newline at end of file diff --git a/content/project/echostack_software/index.md b/content/project/echostack_software/index.md new file mode 100644 index 00000000000..2489d1bc5cd --- /dev/null +++ b/content/project/echostack_software/index.md @@ -0,0 +1,55 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "The open-source \"Echostack\" for scalable, cloud-native processing of water column sonar data" +date: 2021-07-01 +authors: +slug: echostack +weight: 15 +draft: false +tags: + - fisheries acoustics + - scientific computing + - cloud computing + - open-source + - community engagement +summary: "Enhancing the processing capacity and efficiency for echosounder data." + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +Water column sonar data collected by echosounders are essential for fisheries and marine ecosystem research, enabling the detection, classification, and quantification of fish and zooplankton from many different ocean observing platforms. However, the broad usage of these data has been hindered by the lack of modular software tools that allow flexible composition of data processing workflows that incorporate powerful analytical tools in the scientific Python ecosystem. We address this gap by developing **Echostack**, a suite of open-source Python software packages that leverage existing distributed computing and cloud-interfacing libraries to support intuitive and scalable data access, processing, and interpretation. These tools can be used individually or orchestrated together, which we demonstrate in example use cases for a fisheries acoustic-trawl survey. + +Currently, the Echostack contains the following packages: +- [Echopype](https://github.com/OSOceanAcoustics/echopype): performs data standardization and computation from raw instrument files to acoustic data products + - Check out the [Echopype paper in ICES Journal of Marine Science](https://doi.org/10.1093/icesjms/fsae133) +- [Echopop](https://github.com/OSOceanAcoustics/echopop): generates acoustically derived biological estimates, such as abundance + - Learn more on [Echopop project page](../../project_others/echopop/) +- [Echoshader](https://github.com/OSOceanAcoustics/echoshader): enables interactive acoustic data visualization and exploration +- [Echoregions](https://github.com/OSOceanAcoustics/echoregions): interfaces acoustic data with machine learning developments +- [Echodataflow](https://github.com/OSOceanAcoustics/echodataflow): workflow orchestration via text-based configuration “recipes” instead of code + +These packages are accompanied by a set of data processing level definitions, [Echolevels](https://github.com/OSOceanAcoustics/echolevels), which categorizes data products at different workflow stages to enhance data understanding and provenance tracking. + +Check out Wu-Jung's talk at SciPy 2024 and the associated [proceeding paper](https://doi.org/10.25080/WXRH8633)! +{{< youtube YRFxMGisGww >}} + + +**Funding**: +- NOAA Fisheries +- NOAA Office of Ocean Exploration and Research [FY2021 grants](https://oceanexplorer.noaa.gov/news/oer-updates/2021/fy21-ffo-schedule.html) \ No newline at end of file diff --git a/content/project/ubna_pam/index.md b/content/project/ubna_pam/index.md new file mode 100644 index 00000000000..19550e24a40 --- /dev/null +++ b/content/project/ubna_pam/index.md @@ -0,0 +1,38 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ +title: "Passive acoustic monitoring of bats in the Union Bay Natural Area" +date: 2021-09-01 +authors: +slug: ubna-pam +weight: 10 +draft: false +tags: + - echolocation + - passive acoustic monitoring + - community engagement +summary: "Using passive acoustic techniques to monitor bat activity on UW campus!" + +# Customize +share: false +markup: md +math: true +featured: false + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: + Placement options: 1 + focal_point: "Center" + preview_only: true + +--- + +Understanding how echolocators make use of sound to navigate their surroundings has great potential for informing the design of advanced acoustic sensing technologies. Although much has already been studied in laboratory experiments, technology has just started catching up to allow researchers to study echolocation-related processes in the wild. Advancements in passive acoustic monitoring tools have made it affordable to conduct long-term acoustic surveys on animals in the wild. Echolocators, like bats, are well-suited for monitoring using simple passive acoustic techniques because of their use of acoustics and navgitaion in air. + +In this project, we sought to collect long-term acoustic data using Audiomoths from an urban natural area called the Union Bay Natural Area at the University of Washington. With this data, we hope to uncover questions on how environmental conditions influence how bats choose to forage. + +**Funding**: [UW Royalty Research Fund](https://www.washington.edu/research/or/royalty-research-fund-rrf/) diff --git a/content/project/2021-cloud-workflows/index.md b/content/project_others/2021-cloud-workflows/index.md similarity index 100% rename from content/project/2021-cloud-workflows/index.md rename to content/project_others/2021-cloud-workflows/index.md diff --git a/content/project/2022-ubna-pam/index.md b/content/project_others/2022-ubna-pam/index.md similarity index 100% rename from content/project/2022-ubna-pam/index.md rename to content/project_others/2022-ubna-pam/index.md diff --git a/content/project/2022-muri-echolocation/index.md b/content/project_others/2024-muri-echolocation/index.md similarity index 93% rename from content/project/2022-muri-echolocation/index.md rename to content/project_others/2024-muri-echolocation/index.md index bf631bb396a..04d364979d3 100644 --- a/content/project/2022-muri-echolocation/index.md +++ b/content/project_others/2024-muri-echolocation/index.md @@ -5,7 +5,7 @@ date: 2022-07-01T14:50:00-08:00 authors: slug: 2024-muri-echolocation weight: 40 -draft: false +draft: true tags: - animal echolocation - toothed whales @@ -34,4 +34,4 @@ image: The present study aims to develop physics-based models that enable a better understanding of the directional hearing mechanisms in toothed whales. The proposed models will help elucidate the complex acoustic pathways that play a crucial role in the ability of these marine mammals to locate and track prey, communicate with conspecifics, and avoid potential threats in their environment. We intend to employ a range of analytical and computational techniques to model the sound propagation and reception in the auditory systems of toothed whales, which will provide valuable insights into their hearing capabilities. The ultimate goal of this research is to enhance our knowledge of the sensory systems of toothed whales, which could have significant implications for their conservation and management in the wild, as well as for the development of innovative technologies inspired by nature. -**Funding agency**: Office of Naval Research -- Multidisciplinary University Research Initiative (MURI) +**Funding**: Office of Naval Research -- Multidisciplinary University Research Initiative (MURI) diff --git a/content/project/2024-ubna-weather/index.md b/content/project_others/2024-ubna-weather/index.md similarity index 100% rename from content/project/2024-ubna-weather/index.md rename to content/project_others/2024-ubna-weather/index.md diff --git a/content/software/_index.md b/content/project_others/_index.md similarity index 87% rename from content/software/_index.md rename to content/project_others/_index.md index ea521d70e8d..49b6fd0bec9 100644 --- a/content/software/_index.md +++ b/content/project_others/_index.md @@ -1,12 +1,12 @@ --- -title: Software +title: Project # View. # 1 = List # 2 = Compact # 3 = Card # 4 = Citation -view: 3 +view: 2 # Optional header image (relative to `static/img/` folder). header: diff --git a/content/project/2021-echopro/index.md b/content/project_others/echopop/index.md similarity index 93% rename from content/project/2021-echopro/index.md rename to content/project_others/echopop/index.md index bd94855e584..63834d25268 100644 --- a/content/project/2021-echopro/index.md +++ b/content/project_others/echopop/index.md @@ -1,17 +1,16 @@ --- # Documentation: https://sourcethemes.com/academic/docs/managing-content/ -title: "Echopop: hake biomass estimation" +title: "Echopop: biomass estimation for Pacific Hake" date: 2022-01-25T17:02:36-08:00 authors: -slug: 2021-echopro +slug: echopop weight: 17 draft: false tags: - fisheries acoustics - - biomass estimation - - community engagement - - software development -summary: "Modernizing the EchoPro workflow for integrating acoustic and biological survey samples for biomass estimation." + - scientific computing + - open-source +summary: "Integrating echosounder data and net catches for biomass estimation." # Customize share: false diff --git a/content/software/echopype/featured.png b/content/project_others/echopype/featured.png similarity index 100% rename from content/software/echopype/featured.png rename to content/project_others/echopype/featured.png diff --git a/content/software/echopype/index.md b/content/project_others/echopype/index.md similarity index 96% rename from content/software/echopype/index.md rename to content/project_others/echopype/index.md index ee0ef11c20e..4f6cc359234 100644 --- a/content/software/echopype/index.md +++ b/content/project_others/echopype/index.md @@ -7,9 +7,9 @@ slug: echopype weight: 30 draft: false tags: - - python + - fisheries acoustics + - scientific computing - open-source - - echosounder summary: "A Python package that enhances the interoperability and scalability in ocean sonar processing." # Customize diff --git a/content/publication/2021-lee-etal-echopype/index.md b/content/publication/2021-lee-etal-echopype/index.md deleted file mode 100644 index db0eba83146..00000000000 --- a/content/publication/2021-lee-etal-echopype/index.md +++ /dev/null @@ -1,79 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: "Echopype: A Python library for interoperable and scalable processing of water column sonar data for biological information" -authors: ["W-J Lee", "E Mayorga", "L Setiawan", "I Majeed", "K Nguyen", "V Staneva"] -date: 2021-10-30T09:00:00 -# doi: "https://arxiv.org/abs/2111.00187" - -# Customize -share: false -markup: md -math: true - - -# Schedule page publish date (NOT publication's date). -publishDate: 2020-10-30T08:30:00-08:00 - -# Publication type. -# Legend: 0 = Uncategorized; 1 = Conference paper; 2 = Journal article; -# 3 = Preprint / Working Paper; 4 = Report; 5 = Book; 6 = Book section; -# 7 = Thesis; 8 = Patent -publication_types: ["3"] - -# Publication name and optional abbreviated publication name. -publication: "arXiv" -publication_short: "arXiv" - -abstract: "High-frequency sonar systems deployed on a broad variety of ocean observing platforms are creating a deluge of water column sonar data at unprecedented speed from all corners of the ocean. Efficient and integrative analysis of these data, either across different sonar instruments or with other oceanographic datasets, holds the key to monitoring and understanding the response of marine organisms to the rapidly changing environments. In this paper we present echopype, an open-source Python software library designed to address this need. By standardizing water column sonar data from diverse instrument sources following a community convention and utilizing the widely embraced netCDF data model to encode sonar data as labeled, multi-dimensional arrays, echopype facilitates intuitive, user-friendly exploration and use of sonar data in an instrument-agnostic manner. Through leveraging existing open-source Python libraries optimized for distributed computing, echopype directly enables computational interoperability and scalability in both local and cloud computing environments. Echopype's modularized package structure further provides a conceptually unified implementation framework for expanding its support for additional instrument raw data formats and incorporating new data analysis and visualization functionalities. We envision the continued development of echopype as a catalyst for making information derived from water column sonar data an integrated component of regional and global ocean observation strategies." - -# Summary. An optional shortened abstract. -summary: " " - -tags: [] -categories: ["sonar"] -featured: false - -# Custom links (optional). -# Uncomment and edit lines below to show custom links. -# links: -# - name: Follow -# url: https://twitter.com -# icon_pack: fab -# icon: twitter -links: -- name: arXiv - url: https://arxiv.org/abs/2111.00187 -url_code: -url_dataset: -url_poster: -url_project: -url_slides: -url_source: -url_video: - -# Featured image -# To use, place an image named `featured.jpg/png` in your page's folder. -# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width -# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight -# Set `preview_only` to `true` to just use the image for thumbnails. -image: - caption: "" - Placement options: 1 - focal_point: "Center" - preview_only: false - -# Associated Projects (optional). -# Associate this publication with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `internal-project` references `content/project/internal-project/index.md`. -# Otherwise, set `projects: []`. -projects: [] - -# Slides (optional). -# Associate this publication with Markdown slides. -# Simply enter your slide deck's filename without extension. -# E.g. `slides: "example"` references `content/slides/example/index.md`. -# Otherwise, set `slides: ""`. -slides: "" ---- diff --git a/content/publication/2024-lee-etal-echopype/index.md b/content/publication/2024-lee-etal-echopype/index.md new file mode 100644 index 00000000000..234b31f93af --- /dev/null +++ b/content/publication/2024-lee-etal-echopype/index.md @@ -0,0 +1,81 @@ +--- +# Documentation: https://sourcethemes.com/academic/docs/managing-content/ + +title: "Interoperable and scalable echosounder data processing with Echopype" +authors: ["W-J Lee", "L Setiawan", "C Tuguinay", "E Mayorga", "V Staneva"] +date: 2024-10-09 +doi: "10.1093/icesjms/fsae133" + +# Customize +share: false +markup: md +math: true + + +# Schedule page publish date (NOT publication's date). +publishDate: 2020-10-09 + +# Publication type. +# Legend: 0 = Uncategorized; 1 = Conference paper; 2 = Journal article; +# 3 = Preprint / Working Paper; 4 = Report; 5 = Book; 6 = Book section; +# 7 = Thesis; 8 = Patent +publication_types: ["2"] + +# Publication name and optional abbreviated publication name. +publication: "ICES Journal of Marine Science" +publication_short: "ICES JMS" + +abstract: "Echosounders are high-frequency sonar systems used to sense fish and zooplankton underwater. Their deployment on a variety of ocean observing platforms is generating vast amounts of data at an unprecedented speed from the oceans. Efficient and integrative analysis of these data, whether across different echosounder instruments or in combination with other oceanographic datasets, is crucial for understanding marine ecosystem response to the rapidly changing climate. Here we present Echopype, an open-source Python software library designed to address this need. By standardizing data as labeled, multi-dimensional arrays encoded in the widely embraced netCDF data model following a community convention, Echopype enhances the interoperability of echosounder data, making it easier to explore and use. By leveraging scientific Python libraries optimized for distributed computing, Echopype achieves computational scalability, enabling efficient processing in both local and cloud computing environments. Echopype’s modularized package structure further provides a unified framework for expanding support for additional instrument raw data formats and incorporating new analysis functionalities. We plan to continue developing Echopype by supporting and collaborating with the echosounder user community, and envision that the growth of this package will catalyze the integration of echosounder data into broader regional and global ocean observation strategies." + +# Summary. An optional shortened abstract. +summary: " " + +tags: + - open-source + - fisheries acoustics + - scientific computing + - community engagement +categories: ["sonar"] +featured: false + +# Custom links (optional). +# Uncomment and edit lines below to show custom links. +# links: +# - name: Follow +# url: https://twitter.com +# icon_pack: fab +# icon: twitter +links: +url_code: +url_dataset: +url_poster: +url_project: +url_slides: +url_source: +url_video: + +# Featured image +# To use, place an image named `featured.jpg/png` in your page's folder. +# Placement options: 1 = Full column width, 2 = Out-set, 3 = Screen-width +# Focal point options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight +# Set `preview_only` to `true` to just use the image for thumbnails. +image: + caption: "" + Placement options: 1 + focal_point: "Center" + preview_only: false + +# Associated Projects (optional). +# Associate this publication with one or more of your projects. +# Simply enter your project's folder or file name without extension. +# E.g. `internal-project` references `content/project/internal-project/index.md`. +# Otherwise, set `projects: []`. +projects: [] + +# Slides (optional). +# Associate this publication with Markdown slides. +# Simply enter your slide deck's filename without extension. +# E.g. `slides: "example"` references `content/slides/example/index.md`. +# Otherwise, set `slides: ""`. +slides: "" +--- diff --git a/content/talk/_index.md b/content/talk/_index.md index 7d27cb39b3f..8c1197ca70e 100644 --- a/content/talk/_index.md +++ b/content/talk/_index.md @@ -1,5 +1,5 @@ --- -title: Recent & Upcoming Talks +title: Presentations # View. # 1 = List diff --git a/content/values/_index.md b/content/values/_index.md deleted file mode 100644 index 681944e18e4..00000000000 --- a/content/values/_index.md +++ /dev/null @@ -1,15 +0,0 @@ ---- -title: Our values - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" - ---- diff --git a/layouts/partials/page_metadata.html b/layouts/partials/page_metadata.html new file mode 100644 index 00000000000..31cfdc2781c --- /dev/null +++ b/layouts/partials/page_metadata.html @@ -0,0 +1,67 @@ +{{ $is_list := .is_list }} +{{ $page := .page }} + +
+ + {{/* If `authors` is set and is not empty. */}} + {{ if $page.Params.authors }} + {{ $authorLen := len $page.Params.authors }} + {{ if gt $authorLen 0 }} +
+ {{ partial "page_metadata_authors" $page }} +
+ {{ end }} + {{ end }} + + {{ if not (in (slice "talk" "page" "project" "group") $page.Type) }} + + {{ $date := $page.Lastmod.Format site.Params.date_format }} + {{ if eq $page.Type "publication" }} + {{ $date = $page.Date.Format (site.Params.publications.date_format | default "January, 2006") }} + {{ else }} + {{ if ne $page.Params.Lastmod $page.Params.Date }} + {{ i18n "last_updated" }} + {{ end }} + {{ end }} + {{ $date }} + + {{ end }} + + {{ if and (eq $is_list 1) (eq $page.Type "publication") }} + + + {{ if $page.Params.publication_short }} + {{ $page.Params.publication_short | markdownify }} + {{ else if $page.Params.publication }} + {{ $page.Params.publication | markdownify }} + {{ end }} + + {{ end }} + + {{ if and (eq $page.Type "post") (not (or (eq site.Params.reading_time false) (eq $page.Params.reading_time false))) }} + + + {{ $page.ReadingTime }} {{ i18n "minute_read" }} + + {{ end }} + + {{/* Show Disqus comment count if enabled. */}} + {{ $disqus_enabled := eq site.Params.comments.engine 1 | and (index site.Params.comments.commentable $page.Type) | and (ne $page.Params.commentable false) | or $page.Params.commentable }} + {{ if and $disqus_enabled (site.Params.comments.disqus.show_count | default true) }} + + + {{ end}} + + {{ $taxonomy := "categories" }} + {{ if $page.Param $taxonomy }} + + + + {{- range $index, $value := ($page.GetTerms $taxonomy) -}} + {{- if gt $index 0 }}, {{ end -}} + {{ .LinkTitle }} + {{- end -}} + + {{ end }} + +
diff --git a/themes/academic/exampleSite/content/home/posts.md b/themes/academic/exampleSite/content/home/posts.md index 0071af269ab..3b00cc8ec00 100644 --- a/themes/academic/exampleSite/content/home/posts.md +++ b/themes/academic/exampleSite/content/home/posts.md @@ -7,7 +7,7 @@ headless = true # This file represents a page section. active = true # Activate this widget? true/false weight = 60 # Order that this section will appear. -title = "Recent Posts" +title = "Posts" subtitle = "" [content] diff --git a/themes/academic/exampleSite/content/home/publications.md b/themes/academic/exampleSite/content/home/publications.md index b0d7d214db3..6e9ba825aa6 100644 --- a/themes/academic/exampleSite/content/home/publications.md +++ b/themes/academic/exampleSite/content/home/publications.md @@ -7,7 +7,7 @@ headless = true # This file represents a page section. active = true # Activate this widget? true/false weight = 90 # Order that this section will appear. -title = "Recent Publications" +title = "Publications" subtitle = "" [content] diff --git a/themes/academic/i18n/en.yaml b/themes/academic/i18n/en.yaml index fa82e6db13e..581717e9401 100644 --- a/themes/academic/i18n/en.yaml +++ b/themes/academic/i18n/en.yaml @@ -111,7 +111,7 @@ translation: See all posts - id: more_talks - translation: See all talks + translation: See all presentations - id: more_publications translation: See all publications