From 860f6e3a3f11aaaaf2c7d4a59a0cfef919042b01 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:07:38 -0500 Subject: [PATCH 1/9] fix serve command in readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 091def6..0527126 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ Website for Flatiron CCN's NeuroRSE group - Install Jekyll's [requirements](https://jekyllrb.com/docs/installation/) - From the root directory, run `gem install jekyll bundler`, which will install jekyll and the other required packages. -- From the root directory, run `bundle exec jekyll serve -s ./site -d ./_site - --livereload`, then open `localhost:4000` in your browser +- From the root directory, run `bundle exec jekyll serve --livereload`, then + open `localhost:4000` in your browser ## Helpful resources From d8062c7667cd92ba0def66e6f669a00c61ba9804 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:07:49 -0500 Subject: [PATCH 2/9] adds 2025 internship --- _config.yml | 1 - .../2023-11-17-summer-2024-internship.md | 2 +- .../2025-01-06-summer-2025-internship.md | 47 +++++++++++++++++++ 3 files changed, 48 insertions(+), 2 deletions(-) create mode 100644 site/_posts/2025-01-06-summer-2025-internship.md diff --git a/_config.yml b/_config.yml index 8693b29..2202fad 100644 --- a/_config.yml +++ b/_config.yml @@ -41,7 +41,6 @@ collections: - pynapple.md - CCN_Template.md -future: true markdown: kramdown kramdown: parse_block_html: html diff --git a/site/_posts/2023-11-17-summer-2024-internship.md b/site/_posts/2023-11-17-summer-2024-internship.md index 5ca5160..3b082c3 100644 --- a/site/_posts/2023-11-17-summer-2024-internship.md +++ b/site/_posts/2023-11-17-summer-2024-internship.md @@ -1,6 +1,6 @@ --- layout: post -title: "Neuroscience Software Summer Internship" +title: "2024 Neuroscience Software Summer Internship" categories: events --- diff --git a/site/_posts/2025-01-06-summer-2025-internship.md b/site/_posts/2025-01-06-summer-2025-internship.md new file mode 100644 index 0000000..856e523 --- /dev/null +++ b/site/_posts/2025-01-06-summer-2025-internship.md @@ -0,0 +1,47 @@ +--- +layout: post +title: "2025 Neuroscience Software Summer Internship" +categories: events +--- + +Come work with us on an open source neuroscience software package in Manhattan for a summer! The [NeuroRSE team](https://neurorse.flatironinstitute.org/) at the Flatiron Institute Center for Computational Neuroscience is looking for paid interns for Summer 2025. Interns will spend the summer living and working in New York City. + +[Apply here by Jan 17!](https://apply.interfolio.com/159680) + +## What would you work on? +The specific project you will work on will be determined in close consultation with your mentor, a member of the NeuroRSE team. This process will involve finding a good fit between your interests/background and the goals set out in the roadmap for the package you are working on. You can check out the GitHub repositories for each package below to get a sense of the range of possibilities. It is okay if you are not sure exactly what you want to work on before you start; we do not expect applicants to have experience with the packages before applying. + +## Software packages +The three software packages that are currently in development at CCN are: + +![Nemos](/assets/nemos_logo.svg) + +[nemos](https://github.com/flatironinstitute/nemos), maintained by Edoardo Balzani, is a statistical modeling framework for neurophysiology data. + +![plenoptic](/assets/plenoptic_logo.svg) + +[plenoptic](https://github.com/LabForComputationalVision/plenoptic), maintained by Billy Broderick, is a library for model-based visual and auditory stimulus synthesis. + +![pynapple](/assets/pynapple_logo.svg) +{:style="width:50%"} + +[Pynapple](https://github.com/pynapple-org/pynapple) (Python Neural Analysis Package), maintained by Guillaume Viejo, is a library for neurophysiological time series data analysis and visualization. + +## What types of background are we looking for? +We are looking for interns who have experience in at least one of: + +- Using Python packages for scientific computing (e.g., matplotlib, numpy, scikit-learn, etc.). +- Open-source software development (e.g., git, pull request workflow, writing documentation, etc.). +- The relevant neuroscience domain (e.g., calcium image analysis, fitting models to neuroscience data) with *some* programming background. + +We *do not* expect you to already be an expert in both neuroscience and software development! If the internship sounds exciting to you, and you are worried about your qualifications, we recommend that you apply. One of the goals of the internship is to help people learn to contribute to open-source projects. We don't expect you to already be an expert. + +## Anything else I should know? +- The application to work with the NeuroRSE team will be part of the broader CCN intern application. If you specifically want to work with us, please mention that in your application, as well as one or two packages from the above list that you would be interested in working on, and why. +- If you have a GitHub, GitLab, or similar profile, please include a link to the profile in your application. If you have a specific project or two that is particularly relevant, please include a link to those as well. + +## Fine print +Elibigle to current students at Bachelor's level or above. Applications will be accepted starting December 2, 2024. You will be paid $20 - $25 per hour, depending on whether you are an undergraduate or graduate student. Travel, housing, and meals will be provided for all interns. We especially encourage applications from underrepresented populations in the open-source community. + +## To apply +To submit an application, please visit [the Simons website](https://apply.interfolio.com/159680). Deadline for application is **January 17, 2025**. Applications are structured so that you need to put a PI at CCN as primary group and NeuroRSE as secondary group: the written part of the application will clarify your intentions to work on software development. While it is not essential, we recommend that if you are most interested in working on Nemos that you put Alex Williams as the primary group; those interested in Plenoptic or Pynapple should list Eero Simoncelli. From 83cc2121be9732e8dcd23ef431c4854dcf46f83a Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:13:15 -0500 Subject: [PATCH 3/9] fixes Eric's website --- site/_people/thomson.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/site/_people/thomson.md b/site/_people/thomson.md index 4bf9fc1..2702220 100644 --- a/site/_people/thomson.md +++ b/site/_people/thomson.md @@ -1,7 +1,7 @@ --- name: Eric Thomson short_name: thomson -external_url: http://ericthomson.net +external_url: http://www.ericthomson.net picture: /assets/eric.jpg --- Eric helped maintain CaImAn, the calcium imaging analysis platform. His main goal is to build software that works well and is accessible to experimentalists. He received his PhD in neuroscience from UCSD before working as a postdoc at Duke University with Miguel Nicolelis on sensory prosthetic systems. He then worked in computational optics with Roarke Horstmeyer and Eva Naumann, helping to develop a multi-camera microscope system. Before coming to Flatiron, Eric was a data scientist at NIH/NIEHS, working with multiple neuroscience labs to analyze calcium imaging and electrophysiology data. From 9057b2470ba38f632fc372e1f33584e2b851955e Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:25:04 -0500 Subject: [PATCH 4/9] use drafts, not future --- _config.yml | 1 + site/{_posts => _drafts}/2025-01-06-summer-2025-internship.md | 0 2 files changed, 1 insertion(+) rename site/{_posts => _drafts}/2025-01-06-summer-2025-internship.md (100%) diff --git a/_config.yml b/_config.yml index 7db65e7..6808d25 100644 --- a/_config.yml +++ b/_config.yml @@ -42,6 +42,7 @@ collections: - pynapple.md - CCN_Template.md +future: true markdown: kramdown kramdown: parse_block_html: html diff --git a/site/_posts/2025-01-06-summer-2025-internship.md b/site/_drafts/2025-01-06-summer-2025-internship.md similarity index 100% rename from site/_posts/2025-01-06-summer-2025-internship.md rename to site/_drafts/2025-01-06-summer-2025-internship.md From 8fb15c807e56bd66fff7d26b3950bf2a69fbc7c2 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:25:08 -0500 Subject: [PATCH 5/9] adds kramdown parser gfm not necessary for github actions, but I think is necessary forr local --- Gemfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 906e967..1f40d11 100644 --- a/Gemfile +++ b/Gemfile @@ -33,4 +33,6 @@ gem "webrick" gem "logger" gem "csv" gem "ostruct" -gem "base64" \ No newline at end of file +gem "base64" + +gem "kramdown-parser-gfm" From fead90ac1eb8cc8eedf2aca7dd0343de5fa981b8 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Thu, 2 Jan 2025 12:27:33 -0500 Subject: [PATCH 6/9] adds info about drafts to readme --- README.md | 4 ++++ site/_drafts/.gitkeep | 0 2 files changed, 4 insertions(+) create mode 100644 site/_drafts/.gitkeep diff --git a/README.md b/README.md index 894106d..5f5bb2c 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,10 @@ Website for Flatiron CCN's NeuroRSE group - The "Posts" section contains all the files from `site/_posts` whose names must be of the form `YYYY-MM-DD-title.md` in order to be included in the built site. +- If you write a post that you do not want rendered yet, save it in the + `site/_drafts` folder. Then, to render it when building locally, add `--drafts` to + the `jekyll serve` command below to see it. When you are ready to include it + on the site, move it to the `site/_posts` folder. ## Building locally diff --git a/site/_drafts/.gitkeep b/site/_drafts/.gitkeep new file mode 100644 index 0000000..e69de29 From 22ae70369577066dbe0d89049d055079827d8757 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Tue, 7 Jan 2025 14:22:39 -0500 Subject: [PATCH 7/9] modifies how we describe people --- site/_drafts/2025-01-06-summer-2025-internship.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/site/_drafts/2025-01-06-summer-2025-internship.md b/site/_drafts/2025-01-06-summer-2025-internship.md index 856e523..6cddf0a 100644 --- a/site/_drafts/2025-01-06-summer-2025-internship.md +++ b/site/_drafts/2025-01-06-summer-2025-internship.md @@ -16,16 +16,21 @@ The three software packages that are currently in development at CCN are: ![Nemos](/assets/nemos_logo.svg) -[nemos](https://github.com/flatironinstitute/nemos), maintained by Edoardo Balzani, is a statistical modeling framework for neurophysiology data. +[nemos](https://github.com/flatironinstitute/nemos) is a statistical modeling framework for neurophysiology data. ![plenoptic](/assets/plenoptic_logo.svg) -[plenoptic](https://github.com/LabForComputationalVision/plenoptic), maintained by Billy Broderick, is a library for model-based visual and auditory stimulus synthesis. +[plenoptic](https://github.com/LabForComputationalVision/plenoptic) is a library for model-based visual and auditory stimulus synthesis. ![pynapple](/assets/pynapple_logo.svg) {:style="width:50%"} -[Pynapple](https://github.com/pynapple-org/pynapple) (Python Neural Analysis Package), maintained by Guillaume Viejo, is a library for neurophysiological time series data analysis and visualization. +[Pynapple](https://github.com/pynapple-org/pynapple) (Python Neural Analysis Package) is a library for neurophysiological time series data analysis and visualization. + +## Who are we? + +{% assign members = "balzani,broderick,venditto,viejo" | split: "," %} +{% include people_list.html people=members %} ## What types of background are we looking for? We are looking for interns who have experience in at least one of: @@ -37,7 +42,7 @@ We are looking for interns who have experience in at least one of: We *do not* expect you to already be an expert in both neuroscience and software development! If the internship sounds exciting to you, and you are worried about your qualifications, we recommend that you apply. One of the goals of the internship is to help people learn to contribute to open-source projects. We don't expect you to already be an expert. ## Anything else I should know? -- The application to work with the NeuroRSE team will be part of the broader CCN intern application. If you specifically want to work with us, please mention that in your application, as well as one or two packages from the above list that you would be interested in working on, and why. +- The application to work with the NeuroRSE team will be part of the broader CCN intern application. If you specifically want to work with us, **please mention** that in your application, as well as one or two packages from the above list that you would be interested in working on, and why. - If you have a GitHub, GitLab, or similar profile, please include a link to the profile in your application. If you have a specific project or two that is particularly relevant, please include a link to those as well. ## Fine print From d09116d6d3247e868805f5f14b34375df10b7e76 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Tue, 7 Jan 2025 14:24:51 -0500 Subject: [PATCH 8/9] moves to posts, moves us to bottom --- .../2025-01-06-summer-2025-internship.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename site/{_drafts => _posts}/2025-01-06-summer-2025-internship.md (100%) diff --git a/site/_drafts/2025-01-06-summer-2025-internship.md b/site/_posts/2025-01-06-summer-2025-internship.md similarity index 100% rename from site/_drafts/2025-01-06-summer-2025-internship.md rename to site/_posts/2025-01-06-summer-2025-internship.md index 6cddf0a..56bcb10 100644 --- a/site/_drafts/2025-01-06-summer-2025-internship.md +++ b/site/_posts/2025-01-06-summer-2025-internship.md @@ -27,11 +27,6 @@ The three software packages that are currently in development at CCN are: [Pynapple](https://github.com/pynapple-org/pynapple) (Python Neural Analysis Package) is a library for neurophysiological time series data analysis and visualization. -## Who are we? - -{% assign members = "balzani,broderick,venditto,viejo" | split: "," %} -{% include people_list.html people=members %} - ## What types of background are we looking for? We are looking for interns who have experience in at least one of: @@ -50,3 +45,8 @@ Elibigle to current students at Bachelor's level or above. Applications will be ## To apply To submit an application, please visit [the Simons website](https://apply.interfolio.com/159680). Deadline for application is **January 17, 2025**. Applications are structured so that you need to put a PI at CCN as primary group and NeuroRSE as secondary group: the written part of the application will clarify your intentions to work on software development. While it is not essential, we recommend that if you are most interested in working on Nemos that you put Alex Williams as the primary group; those interested in Plenoptic or Pynapple should list Eero Simoncelli. + +## Who are we? + +{% assign members = "balzani,broderick,venditto,viejo" | split: "," %} +{% include people_list.html people=members %} From 76a8fddc43b48d4aab255dab2930488dd7dc98de Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Tue, 7 Jan 2025 15:30:11 -0500 Subject: [PATCH 9/9] fix failing htmlproofer - replace old luce scholars link - corrects failure for link rel=canonical on new pages --- .github/workflows/jekyll-gh-pages.yml | 6 +++--- _config.yml | 2 +- site/_people/broderick.md | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml index bcafae8..fc12ec8 100644 --- a/.github/workflows/jekyll-gh-pages.yml +++ b/.github/workflows/jekyll-gh-pages.yml @@ -42,10 +42,10 @@ jobs: - name: Check html uses: chabad360/htmlproofer@master with: - directory: "./_site" # The directory to scan - arguments: --no-enforce-https --allow_hash_href --ignore-missing-alt --assume_extension - ./_site --ignore-urls '/http:\/\/www.hluce.org/' --ignore-files '/.+\/assets\/.+/' - # The arguments to pass to HTMLProofer + directory: "./_site" + # The arguments to pass to HTMLProofer. swap-urls is because of this issue: https://github.com/gjtorikian/html-proofer/issues/170 and basically turns all absolute links from our site that point to our site into relative + arguments: --no-enforce-https --allow_hash_href --ignore-missing-alt --assume_extension - ./_site --ignore-files '/.+\/assets\/.+/' --swap-urls "https?\:\/\/(localhost\:4000|neurorse\.flatironinstitute\.org):" - name: Upload artifact uses: actions/upload-pages-artifact@v2 diff --git a/_config.yml b/_config.yml index 6808d25..ad0d6b2 100644 --- a/_config.yml +++ b/_config.yml @@ -22,7 +22,7 @@ source: site title: NeuroRSE description: >- # this means to ignore newlines until "baseurl:" baseurl: "" -url: "https://neurorse.flatironinstitute.org/" # the base hostname & protocol for your site, e.g. http://example.com +url: "https://neurorse.flatironinstitute.org" # the base hostname & protocol for your site, e.g. http://example.com # Build settings plugins: diff --git a/site/_people/broderick.md b/site/_people/broderick.md index f4799d8..39bad03 100644 --- a/site/_people/broderick.md +++ b/site/_people/broderick.md @@ -5,4 +5,4 @@ external_url: https://wfbroderick.com picture: /assets/billy.jpg job: Associate Research Scientist, CCN --- -Billy Broderick received his Ph.D. from NYU's Center for Neural Science, where he was advised by Eero Simoncelli and Jon Winawer. During his Ph.D., he studied how vision changes across the visual field using fMRI, psychophysics, and computational models. Before that, he worked as a research assistant at Duke University, spent a year at South China Normal University in Guangzhou, China as a [Luce Scholar](http://www.hluce.org/lsprogram.aspx), and got his B.A. in neuroscience and mathematics at Oberlin College +Billy Broderick received his Ph.D. from NYU's Center for Neural Science, where he was advised by Eero Simoncelli and Jon Winawer. During his Ph.D., he studied how vision changes across the visual field using fMRI, psychophysics, and computational models. Before that, he worked as a research assistant at Duke University, spent a year at South China Normal University in Guangzhou, China as a [Luce Scholar](https://lucescholars.org/), and got his B.A. in neuroscience and mathematics at Oberlin College