Scipy proceedings papers

content/newslist.dat

@@ -8,6 +8,8 @@
 
 **[08/2025]** [Aidan Lee](/author/aidan-lee) joined Echospace as an Undergrad Research Assistant. Welcome!
 
+**[08/2024]** Two papers authored by several Echospace members were published at the SciPy 2024 Conference Proceedings: one on [Echostack](https://proceedings.scipy.org/articles/WXRH8633) and another on [Echodataflow](https://echodataflow.readthedocs.io/en/latest/).
+
 **[07/2024]** Wu-Jung gave a talk on our [Echostack software suite](https://proceedings.scipy.org/articles/WXRH8633) and Valentina presented a poster on the [Echodataflow package](https://proceedings.scipy.org/articles/JXDK4427) at the Scipy 2024 conference.
 
 **[06/2024]** Aditya attended the [BioAcoustic Summer School (SeaBASS) in the University of New Hampshire](https://eos.unh.edu/center-acoustics-research-education/education/bioacoustic-summer-school-seabass) and met some inspiring lecturers and students! Wu-Jung also gave a lecture on Fundamentals of Ocean Acoustics!
@@ -76,3 +78,5 @@
 
 **[09/2021]** Wu-Jung and Linda successfully completed this summer's fieldwork evaluating the use of an ADCP-equipped glider as a biological monitoring tool. Check out [NOAA Exploration's coverage of this mission](https://oceanexplorer.noaa.gov/technology/development-partnerships/21adcp-gliders/welcome.html)!
 
+
+

content/publication/2024-lee-etal-scipy-echostack/index.md

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+---
+# Documentation: https://sourcethemes.com/academic/docs/managing-content/
+
+title: "Echostack: A flexible and scalable open-source software suite for echosounder data processing"
+authors: ["W-J Lee", "V Staneva", "L Setiawan", "E Mayorga", "C Tuguinay", "S Butala", "B Lucca", "D Lei"]
+date: 2024-07-10
+doi: "https://doi.org/10.25080/WXRH8633"
+
+# Customize
+share: false
+markup: md
+math: true
+
+
+# Schedule page publish date (NOT publication's date).
+publishDate: 2024-07-10
+
+# 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: "Proceedings of the 23rd Python in Science Conference"
+publication_short: "SciPy Proceedings"
+
+abstract: "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."
+
+# 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).
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+#   Simply enter your slide deck's filename without extension.
+#   E.g. `slides: "example"` references `content/slides/example/index.md`.
+#   Otherwise, set `slides: ""`.
+slides: ""
+---

content/publication/2024-staneva-etal-scipy-echodataflow/index.md

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+---
+# Documentation: https://sourcethemes.com/academic/docs/managing-content/
+
+title: "Echodataflow: Recipe-based Fisheries Acoustics Workflow Orchestration"
+authors: ["V Staneva", "S Butala", "L Setiawan", "W-J Lee"]
+date: 2024-07-10
+doi: "https://doi.org/10.25080/JXDK4427"
+
+# Customize
+share: false
+markup: md
+math: true
+
+
+# Schedule page publish date (NOT publication's date).
+publishDate: 2024-07-10
+
+# 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: "Proceedings of the 23rd Python in Science Conference"
+publication_short: "SciPy Proceedings"
+
+abstract: "With the influx of large data from multiple instruments and experiments, scientists are wrangling complex data pipelines that are context-dependent and non-reproducible. We demonstrate how we leverage Prefect ([Prefect](https://www.prefect.io/), 2024), a modern orchestration framework, to facilitate fisheries acoustics data processing. We built a Python package Echodataflow ([Echodataflow](https://github.com/OSOceanAcoustics/echodataflow), 2024) which 1) allows users to specify workflows and their parameters through editing text “recipes” which provide transparency and reproducibility of the pipelines; 2) supports scaling of the workflows while abstracting the computational infrastructure; 3) provides monitoring and logging of the workflow progress. Under the hood, Echodataflow uses Prefect to execute the workflows while providing a domain-friendly interface to facilitate diverse fisheries acoustics use cases. We demonstrate the features through a typical ship survey data processing pipeline."
+
+# 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: ""
+---