Update v1-release.md

Author: sehilyi

blog/v1-release.md

@@ -7,10 +7,10 @@ Initiated in 2020, the Gosling project aimed to develop an integrated platform c
 
 To enable flexible visualization creation, we first needed to understand what kinds of genome-mapped data visualizations exist in the wild. Fortunately, HIDIVE Lab produced a taxonomy for genomics data visualization after reviewing hundreds of data visualizations and tools ([Nusrat et al. CGF](https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727)). Adopting the primitive building blocks from the taxonomy (e.g., layouts, arrangements, and alignments), we designed the Gosling grammar for genomics data visualization. The Gosling grammar adopts a computer programming paradigm ([declarative programming](https://en.wikipedia.org/wiki/Declarative_programming)), which enables users to focus more on what they want to create rather than how they want to achieve. Gosling was first published in 2021 ([L’Yi et al. TVCG](https://pmc.ncbi.nlm.nih.gov/articles/PMC8826597/)), describing its five distinctive strengths and introducing its toolkit for JavaScript. Gosling was then extended for Python and computational notebook users ([Gos Python package](https://gosling-lang.github.io/gos/)) with some major usability enhancements, such as transparent data loading ([Manz et al. Bioinformatics](https://academic.oup.com/bioinformatics/article/39/1/btad050/6998203)).
 
-## How Gosling is being used in the community
-Gosling has been widely adopted both in academia and industry. Gosling visualizations were integrated into widely used data portals in cancer genomics, such as [cBioPortal](https://www.cbioportal.org/patient/openResource_CHROMOSCOPE?studyId=pancan_pcawg_2020&caseId=DO2706) and [Cistrome Data Browser](https://db3.cistrome.org/browser/) ([Taing et al. Nucleic Acids Res](https://academic.oup.com/nar/article/52/D1/D61/7424438)). Researchers at Linköping University used Gosling to create stimuli for controlled user experiments ([Ståhlbom et al. CGF](https://onlinelibrary.wiley.com/doi/10.1111/cgf.15102)). A research team at Johannes Kepler University Linz extended Gosling for time-based data. A company [Appsilon](https://www.appsilon.com/) extended Gosling by building its R Shiny wrapper ([Appsilon/shiny.gosling](https://appsilon.github.io/shiny.gosling/)).
+## How Gosling has been used
+Gosling has been widely adopted both in academia and industry. Gosling visualizations were integrated into widely used data portals, such as [cBioPortal](https://www.cbioportal.org/patient/openResource_CHROMOSCOPE?studyId=pancan_pcawg_2020&caseId=DO2706), [REDIportal](http://srv00.recas.ba.infn.it/atlas/), and [Cistrome Data Browser](https://db3.cistrome.org/browser/) ([Taing et al. Nucleic Acids Res](https://academic.oup.com/nar/article/52/D1/D61/7424438)). Researchers at Linköping University used Gosling to create stimuli for controlled user experiments ([Ståhlbom et al. CGF](https://onlinelibrary.wiley.com/doi/10.1111/cgf.15102)). A research team at Johannes Kepler University Linz extended Gosling for time-based data.  A company [Appsilon](https://www.appsilon.com/) extended Gosling by building its R Shiny wrapper ([Appsilon/shiny.gosling](https://appsilon.github.io/shiny.gosling/)).
 
-Given the flexibility of Gosling in building genomics data visualizations and tools, Gosling has been used in many research projects in the HIDIVE Lab as well. In collaboration with Peter J Park’s group at Harvard Medical School, we built [Chromoscope](https://chromoscope.bio/) ([L’Yi et al. Nat Methods](https://www.nature.com/articles/s41592-023-02056-x)) for browsing structural variation at multiple scales with Circos-like whole genome overviews and read-level BAM alignment views. In collaboration with researchers at Harvard T.H. Chan School of Public Health and Dana-Farber Cancer Institute, we built [Cistrome Explorer](https://cisvis.gehlenborglab.org) for interactive visual analysis of large-scale epigenomic data ([L’Yi et al. Bioinformatics](https://academic.oup.com/bioinformatics/article/39/2/btad018/6998202)). Focusing more on visualization and human–computer interaction research, we used Gosling to build the GenoREC ([Pandey et al. VIS 2022](https://ieeexplore.ieee.org/document/9908148)), an automated recommendation system that helps people without much visualization knowledge to find visual representations and user interactions appropriate for their data and tasks. A visual analytics tool powered by machine learning models—DRAVA ([Wang et al. CHI 2023](https://dl.acm.org/doi/full/10.1145/3544548.3581127))—integrated Gosling to provide a spatial context of the whole genome Hi-C matrix in exploring the latent space of its sliding images. Most recently, we explored ideas to combine Gosling with various visualization authoring interfaces, such as natural language interfaces, to lower barriers to creating expressive visualizations in a graphical user interface ([L’Yi et al. VIS 2024](https://ieeexplore.ieee.org/document/10670517) and [van den Brandt et al. VIS 2024](https://ieeexplore.ieee.org/document/10681582)). There are many more exciting projects to be announced soon.
+Given the flexibility of Gosling in building genomics data visualizations and tools, Gosling has been used in many research projects in the HIDIVE Lab as well. In collaboration with Peter J Park’s group at Harvard Medical School, we built [Chromoscope](https://chromoscope.bio/) ([L’Yi et al. Nat Methods](https://www.nature.com/articles/s41592-023-02056-x)) for browsing structural variation at multiple scales with Circos-like whole genome overviews and read-level BAM alignment views. In collaboration with researchers at Harvard T.H. Chan School of Public Health and Dana-Farber Cancer Institute, we built [Cistrome Explorer](https://cisvis.gehlenborglab.org) for interactive visual analysis of large-scale epigenomic data ([L’Yi et al. Bioinformatics](https://academic.oup.com/bioinformatics/article/39/2/btad018/6998202)). Focusing more on visualization and human–computer interaction research, we used Gosling to build the GenoREC ([Pandey et al. VIS 2022](https://ieeexplore.ieee.org/document/9908148)), an automated recommendation system that helps people without much visualization knowledge to find visual representations and user interactions appropriate for their data and tasks. A visual analytics tool powered by machine learning models—DRAVA ([Wang et al. CHI 2023](https://dl.acm.org/doi/full/10.1145/3544548.3581127))—integrated Gosling to provide a spatial context of the whole genome Hi-C matrix in exploring the latent space of its sliding images. Most recently, we explored ideas to combine Gosling with various visualization authoring interfaces, such as natural language interfaces, to lower barriers to creating expressive visualizations in a graphical user interface ([L’Yi et al. VIS 2024](https://ieeexplore.ieee.org/document/10670517) and [van den Brandt et al. VIS 2024](https://ieeexplore.ieee.org/document/10681582)). Aiming to help people with visual impairments, AltGosling automatically generates accessible textual descriptions that describe genomics data visualizations ([Smits et al. Bioinformatics 2024](https://academic.oup.com/bioinformatics/article/40/12/btae670/7900296)). There are many more exciting projects to be announced soon.
 
 ## What v1.0.0 means
 Considering Gosling’s successful and widespread application across a variety of the aforementioned use cases, it’s safe to say that Gosling has reached a certain feature set that’s proven useful in multiple scenarios. As for any software—and academic software nonetheless—there still are some rough edges and unpolished parts of the interface and implementation. We’re going to focus on improving those parts in the upcoming months. At the same time, we’re excited to bring larger changes to Gosling's implementation and features, too. For these reasons, we believe now is the right time to mark this milestone by designating the current state as version 1.0.0. This allows existing software that depends on the current state of Gosling to pin the major version 1, while more experimental projects can follow the minor versions that we’d make in the near future. Thank you for being a part of this journey. Gosling v1.0 is here and ready for you to get started!