From 1c077a7359fb06d0b7362d582b44f5b194cdd1ef Mon Sep 17 00:00:00 2001 From: Yuk Kei Wan <41866052+yuukiiwa@users.noreply.github.com> Date: Sun, 13 Jul 2025 08:18:21 +0800 Subject: [PATCH 1/5] Create yuukiiwa_application_placeholder.yaml --- .../yuukiiwa_application_placeholder.yaml | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 datasets/yuukiiwa_application_placeholder.yaml diff --git a/datasets/yuukiiwa_application_placeholder.yaml b/datasets/yuukiiwa_application_placeholder.yaml new file mode 100644 index 000000000..79146bbb5 --- /dev/null +++ b/datasets/yuukiiwa_application_placeholder.yaml @@ -0,0 +1,30 @@ +Name: Update on August 31 +Description:Update on August 31, 2025 +Documentation: Update on August 31, 2025 +Contact: Update on August 31, 2025 +ManagedBy: "The Genome Institute of Singapore (https://www.a-star.edu.sg/gis) and UMass Chan Medical School's RNA Therapeutics Institute (https://www.umassmed.edu/rti/)" +UpdateFrequency: Datasets will be updated periodically as additional data are generated. +Tags: + - TBD +License: "[CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/)" +Citation: Update on August 31, 2025 +Resources: + - Description: Update on August 31, 2025 + ARN: Update on August 31, 2025 + Region: ap-southeast-1 + Type: S3 Bucket + Explore: + - '[Browse Bucket](http://frag-struc.s3-website-ap-southeast-1.amazonaws.com/)' +DataAtWork: + Tutorials: + - Title: Update on August 31, 2025 + URL: Update on August 31, 2025 + AuthorName: Leonard Schärfen and Yuk Kei Wan + Tools & Applications: + - Title: Update on August 31, 2025 + URL: Update on August 31, 2025 + AuthorName: Leonard Schärfen and Yuk Kei Wan + Publications: + - Title: Update on August 31, 2025 + URL: In Preparation + AuthorName: Leonard Schärfen and Yuk Kei Wan From 9399cf794e460f5eee9bf023cea8d00f7c0d38b9 Mon Sep 17 00:00:00 2001 From: Yuk Kei Wan <41866052+yuukiiwa@users.noreply.github.com> Date: Thu, 31 Jul 2025 11:03:04 +0800 Subject: [PATCH 2/5] update license to CC BY 4 --- datasets/yuukiiwa_application_placeholder.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/datasets/yuukiiwa_application_placeholder.yaml b/datasets/yuukiiwa_application_placeholder.yaml index 79146bbb5..7934e04af 100644 --- a/datasets/yuukiiwa_application_placeholder.yaml +++ b/datasets/yuukiiwa_application_placeholder.yaml @@ -6,7 +6,7 @@ ManagedBy: "The Genome Institute of Singapore (https://www.a-star.edu.sg/gis) an UpdateFrequency: Datasets will be updated periodically as additional data are generated. Tags: - TBD -License: "[CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/)" +License: "[CC BY 4.0](https://creativecommons.org/licenses/by-nc/4.0/)" Citation: Update on August 31, 2025 Resources: - Description: Update on August 31, 2025 From d31361616f6155b17ce70481bb333f0ce4da5d64 Mon Sep 17 00:00:00 2001 From: Yuk Kei Wan <41866052+yuukiiwa@users.noreply.github.com> Date: Thu, 31 Jul 2025 11:05:42 +0800 Subject: [PATCH 3/5] update to CC BY 4.0 --- datasets/yuukiiwa_application_placeholder.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/datasets/yuukiiwa_application_placeholder.yaml b/datasets/yuukiiwa_application_placeholder.yaml index 7934e04af..9f9b79afb 100644 --- a/datasets/yuukiiwa_application_placeholder.yaml +++ b/datasets/yuukiiwa_application_placeholder.yaml @@ -6,7 +6,7 @@ ManagedBy: "The Genome Institute of Singapore (https://www.a-star.edu.sg/gis) an UpdateFrequency: Datasets will be updated periodically as additional data are generated. Tags: - TBD -License: "[CC BY 4.0](https://creativecommons.org/licenses/by-nc/4.0/)" +License: "[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)" Citation: Update on August 31, 2025 Resources: - Description: Update on August 31, 2025 From d2e30aaa52d1c2eefd62502ea5515af1c85f34ac Mon Sep 17 00:00:00 2001 From: Yuk Kei Wan <41866052+yuukiiwa@users.noreply.github.com> Date: Mon, 1 Sep 2025 00:47:05 +0800 Subject: [PATCH 4/5] make bucket public --- .../yuukiiwa_application_placeholder.yaml | 30 --------------- frag-struc.yaml | 37 +++++++++++++++++++ 2 files changed, 37 insertions(+), 30 deletions(-) delete mode 100644 datasets/yuukiiwa_application_placeholder.yaml create mode 100644 frag-struc.yaml diff --git a/datasets/yuukiiwa_application_placeholder.yaml b/datasets/yuukiiwa_application_placeholder.yaml deleted file mode 100644 index 9f9b79afb..000000000 --- a/datasets/yuukiiwa_application_placeholder.yaml +++ /dev/null @@ -1,30 +0,0 @@ -Name: Update on August 31 -Description:Update on August 31, 2025 -Documentation: Update on August 31, 2025 -Contact: Update on August 31, 2025 -ManagedBy: "The Genome Institute of Singapore (https://www.a-star.edu.sg/gis) and UMass Chan Medical School's RNA Therapeutics Institute (https://www.umassmed.edu/rti/)" -UpdateFrequency: Datasets will be updated periodically as additional data are generated. -Tags: - - TBD -License: "[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)" -Citation: Update on August 31, 2025 -Resources: - - Description: Update on August 31, 2025 - ARN: Update on August 31, 2025 - Region: ap-southeast-1 - Type: S3 Bucket - Explore: - - '[Browse Bucket](http://frag-struc.s3-website-ap-southeast-1.amazonaws.com/)' -DataAtWork: - Tutorials: - - Title: Update on August 31, 2025 - URL: Update on August 31, 2025 - AuthorName: Leonard Schärfen and Yuk Kei Wan - Tools & Applications: - - Title: Update on August 31, 2025 - URL: Update on August 31, 2025 - AuthorName: Leonard Schärfen and Yuk Kei Wan - Publications: - - Title: Update on August 31, 2025 - URL: In Preparation - AuthorName: Leonard Schärfen and Yuk Kei Wan diff --git a/frag-struc.yaml b/frag-struc.yaml new file mode 100644 index 000000000..2e9bc7648 --- /dev/null +++ b/frag-struc.yaml @@ -0,0 +1,37 @@ +Name: RNA structure by fragmentation frequency +Description: "The fragSTRUC project devises a software to extract RNA secondary structure information from Illumina datasets, based on divalent ions in standard RNA-seq library preparation fragmenting sequences at non-base-paired regions of RNA." +Documentation: https://github.com/yuukiiwa/RNA_structure_by_fragmentation_frequency +Contact: "[fragSTRUC team](https://github.com/yuukiiwa/RNA_structure_by_fragmentation_frequency)" +ManagedBy: "The Genome Institute of Singapore (https://www.a-star.edu.sg/gis) and UMass Chan Medical School's RNA Therapeutics Institute (https://www.umassmed.edu/rti/)" +UpdateFrequency: Datasets will be updated periodically as additional data is generated. +Tags: + - RNA structure + - genomic + - transcriptomics + - life sciences + - Illumina sequencing + - bulk RNA sequencing + - bioinformatics + - bigwig +License: "[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)" +Citation: "In addition, please cite Yuk Kei Wan and Leonard Schärfen Hidden structural information in RNA sequencing data." +Resources: + - Description: RNA structure by fragmentation frequency + ARN: arn:aws:s3:::frag-struc + Region: ap-southeast-1 + Type: S3 Bucket + Explore: + - '[Browse Bucket](http://frag-struc.s3-website-ap-southeast-1.amazonaws.com/)' +DataAtWork: + Tutorials: + - Title: Accessing the fragSTRUC dataset on AWS + URL: https://github.com/yuukiiwa/RNA_structure_by_fragmentation_frequency/blob/main/README.md + AuthorName: Yuk Kei Wan and Leonard Schärfen + Tools & Applications: + - Title: "fragSTRUC: RNA structure by fragmentation frequency" + URL: https://github.com/lschaerfen/fragstruc + AuthorName: Yuk Kei Wan and Leonard Schärfen + Publications: + - Title: Hidden structural information in RNA sequencing data. + URL: In Preparation + AuthorName: Yuk Kei Wan and Leonard Schärfen From 9ed9a146adfba56c8f86367ba0315ea094b17176 Mon Sep 17 00:00:00 2001 From: berylrab Date: Tue, 2 Sep 2025 14:46:19 -0400 Subject: [PATCH 5/5] ok:Update frag-struc.yaml