diff --git a/assets/main.scss b/assets/main.scss index 4c4f39fb..2bdc58ff 100644 --- a/assets/main.scss +++ b/assets/main.scss @@ -30,7 +30,6 @@ $bluesky-blue: #0a7aff; $overline: #e0e0e0; $linkunderline: #aaaaaa; $backtickbg: #f9f9f9; -$backticktext: #333333; $navtext: #555555; $navtexthover: #000000; @@ -665,12 +664,6 @@ body { } } - span.backticked { - font-family: Inter, sans-serif; - color: $backticktext; - font-weight: 500; - } - p > a { text-decoration: none; color: inherit; @@ -944,10 +937,6 @@ body { > p > img { margin-bottom: 1.5rem; } - span.backticked { - font-size: 1.2rem; - line-height: 1.1rem; - } p, div, ul, diff --git a/content/_index.md b/content/_index.md index bdffb6c8..3890cd50 100644 --- a/content/_index.md +++ b/content/_index.md @@ -70,19 +70,19 @@ description = "Foundational tools for single-cell omics data analysis" [mission] text = """\ -**scverse** is a consortium of foundational tools (mostly in Python) for omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.""" +Scverse is a consortium of foundational tools (mostly in Python) for omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.""" # Ecosystem [ecosystem] text = """\ -A broader ecosystem of packages builds on the **scverse** core packages. [These tools](/packages/#ecosystem) implement models and analytical approaches to tackle challenges in spatial omics, regulatory genomics, trajectory inference, visualization, and more.""" +A broader ecosystem of packages builds on the scverse core packages. [These tools](/packages/#ecosystem) implement models and analytical approaches to tackle challenges in spatial omics, regulatory genomics, trajectory inference, visualization, and more.""" # Team [team] text = """\ -**scverse** is a community project currently governed by the developers of the core packages. Please [reach out](/join) if you'd like to be involved! +Scverse is a community project currently governed by the developers of the core packages. Please [reach out](/join) if you'd like to be involved! """ # People information is recorded in the people/_index.md file @@ -92,7 +92,7 @@ text = """\ [references] text = """\ -**scverse** tools are used in numerous research and industry projects across the globe and are referenced in [thousands](https://scholar.google.ru/scholar?cites=14568046068402025757) of academic publications. Consider consulting the following references for more information about core **scverse** libraries and citing the relevant articles when using them in your work: +Scverse tools are used in numerous research and industry projects across the globe and are referenced in [thousands](https://scholar.google.ru/scholar?cites=14568046068402025757) of academic publications. Consider consulting the following references for more information about core scverse libraries and citing the relevant articles when using them in your work: """ [[references.citations]] diff --git a/content/about/_index.md b/content/about/_index.md index 39fd95de..3086cca0 100644 --- a/content/about/_index.md +++ b/content/about/_index.md @@ -2,13 +2,13 @@ title = "About scverse" +++ -scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools. +Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools. Check out our [introductory blog post](/blog/hello-world) and [mission statement](/about/mission) for more details. ## Sponsorship -scverse is a fiscally sponsored project of NumFOCUS, a nonprofit dedicated to supporting the open-source scientific computing community. +Scverse is a fiscally sponsored project of NumFOCUS, a nonprofit dedicated to supporting the open-source scientific computing community. If you like scverse and want to support our mission, please consider making a [donation](https://numfocus.org/donate-to-scverse) to support our efforts.
diff --git a/content/about/ai_policy/_index.md b/content/about/ai_policy/_index.md index 174551be..f0f8d7ab 100644 --- a/content/about/ai_policy/_index.md +++ b/content/about/ai_policy/_index.md @@ -4,7 +4,7 @@ title = "AI Policy" ## Overview -scverse encourages its users to get involved with the development process, and if a user wishes to write code AI-assisted, that is also great! +Scverse encourages its users to get involved with the development process, and if a user wishes to write code AI-assisted, that is also great! We encourage our users to do what is comfortable for them. However, since AI-assisted coding has led many open source projects to experience a massive increase in low-quality code submissions, we want to clarify our position in this document. diff --git a/content/about/mission/_index.md b/content/about/mission/_index.md index fbdc646c..bef6d401 100644 --- a/content/about/mission/_index.md +++ b/content/about/mission/_index.md @@ -16,31 +16,31 @@ We as scverse® want to make analysis tools for omics data in the life sciences ## Organization and vision The growing adoption of Python for single-cell omics data analysis has been catalyzed by [Scanpy](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0) and [AnnData](https://anndata.readthedocs.io/en/latest/). -Around this infrastructure an ecosystem of packages has been created by various developers and institutions — extending single-cell analysis to different modalities and addressing challenges at the cutting-edge of single-cell research. We believe that progress in this field can't be silo'd to a few groups. To further nurture the growth of this ecosystem, we've formed a new organization -- **`scverse`**. +Around this infrastructure an ecosystem of packages has been created by various developers and institutions — extending single-cell analysis to different modalities and addressing challenges at the cutting-edge of single-cell research. We believe that progress in this field can't be silo'd to a few groups. To further nurture the growth of this ecosystem, we've formed a new organization -- scverse. -`scverse` is a consortium of tools with users and developers across the world. To sustain the utility and growth of the ecosystem, it’s essential that the core analytic tools are robust and well-maintained. This entails consistent support and improvement of tools beyond what's possible in the conventional single-lab academic setting. +Scverse is a consortium of tools with users and developers across the world. To sustain the utility and growth of the ecosystem, it’s essential that the core analytic tools are robust and well-maintained. This entails consistent support and improvement of tools beyond what's possible in the conventional single-lab academic setting. -`scverse` provides high quality infrastructure for analysis of single cell omics data. These *core* tools are well documented, tested, and provide broad functionality. They work with standardized data structures which use common Python numeric types and have interchange-friendly on-disk formats. +Scverse provides high quality infrastructure for analysis of single cell omics data. These *core* tools are well documented, tested, and provide broad functionality. They work with standardized data structures which use common Python numeric types and have interchange-friendly on-disk formats. We define *core* tools as those which facilitate sharing data through common formats, or provide foundational support for single cell datatypes (e.g. modality-specific IO, toolkits) and analyses. -These tools are placed under shared maintenance and development in the `scverse` GitHub organization. +These tools are placed under shared maintenance and development in the scverse GitHub organization. -`scverse` *core* tools are expected to interface with and be supplemented by other tools in the ecosystem. `scverse` strives for synergy and interoperability with the ecosystem of packages built around these *core* tools, to ultimately provide users to cutting-edge and varied selection of analysis methods. +Scverse *core* tools are expected to interface with and be supplemented by other tools in the ecosystem. Scverse strives for synergy and interoperability with the ecosystem of packages built around these *core* tools, to ultimately provide users to cutting-edge and varied selection of analysis methods. ## User engagement -We are community-driven and committed to keeping the `scverse` community open. We strive to actively foster a community where everyone is and feels welcomed, and where there are no barriers to contributions in any form. We welcome newcomers and pledge to build an environment where they can grow as contributors, developers, and community members. Together with technical and development support, we also support our users through: +We are community-driven and committed to keeping the scverse community open. We strive to actively foster a community where everyone is and feels welcomed, and where there are no barriers to contributions in any form. We welcome newcomers and pledge to build an environment where they can grow as contributors, developers, and community members. Together with technical and development support, we also support our users through: * Clear documentation of code and usage via docs and tutorials. * Participation in development through issues and pull requests. * Community forums, such as our Discourse, Zulip, and Twitter. -* Workshops at which we teach analysis workflows based on the `scverse` ecosystem. +* Workshops at which we teach analysis workflows based on the scverse ecosystem. ## Developer engagement -Tools within `scverse` are deliberately not unified under a single package, and instead form a consortium of *core* analytic tools with shared maintenance responsibilities. +Tools within scverse are deliberately not unified under a single package, and instead form a consortium of *core* analytic tools with shared maintenance responsibilities. Development of these packages is not restricted – contributions are welcomed and publicly acknowledged. -However, `scverse` aims to support the external development of new approaches to analyze and work with single cell data. +However, scverse aims to support the external development of new approaches to analyze and work with single cell data. We encourage the creation of new methods and tools on top of the *core* packages and data-structures. We support the development of these ecosystem packages by: @@ -48,7 +48,7 @@ We support the development of these ecosystem packages by: * Providing stable APIs to build on top of. * Providing standardized and well-supported data structure to pass around data. * Making sure all contributions are recognized in our change logs and documentation. -* Promoting 3rd party packages that rely on `scverse` via our websites and social media feeds. +* Promoting 3rd party packages that rely on scverse via our websites and social media feeds. * Establishing open communication channels for: * Discussion and collaboration between developers. * A common forum for user support and engagement. diff --git a/content/about/roles/_index.md b/content/about/roles/_index.md index c6968b51..87cf4cb3 100644 --- a/content/about/roles/_index.md +++ b/content/about/roles/_index.md @@ -50,8 +50,8 @@ There are sub-roles within the core team depending on the kinds covering differe #### Core Developers -Core developers are members of the core team who have made significant code contributions to `scverse`. -They are granted additional rights so they can more easily carry on with their `scverse` related activities. +Core developers are members of the core team who have made significant code contributions to scverse. +They are granted additional rights so they can more easily carry on with their scverse related activities. These rights include: merging approved pull requests, voting for and against contested pull-requests, and being involved in deciding major changes to the API. Core developers are on our [@scverse/core-devs](https://github.com/orgs/scverse/teams/core-devs) GitHub team. @@ -71,7 +71,7 @@ Primary maintainers of new core packages, who are not already core developers, w ### Steering Council The Steering Council (SC) members are core team members who have additional responsibilities to ensure the smooth running of the project. -SC members are expected to participate in strategic planning, approve changes to the governance model, and make decisions about funding granted to `scverse` itself (funding to community members is theirs to pursue and manage). Changes that impact the full project require analysis informed by extensive experience with both the project and the larger ecosystem. +SC members are expected to participate in strategic planning, approve changes to the governance model, and make decisions about funding granted to scverse itself (funding to community members is theirs to pursue and manage). Changes that impact the full project require analysis informed by extensive experience with both the project and the larger ecosystem. When the core team (including the SC members) fails to reach a consensus in a reasonable timeframe, the SC is the entity that resolves the issue. Members of the steering council also have the "owner" role within the [scverse GitHub organization](https://github.com/scverse/) @@ -88,7 +88,7 @@ Nominees should have demonstrated long-term, continued commitment to the project A nomination will result in discussion that cannot take more than a month and then admission to the SC by consensus. During that time deadlocked votes of the SC will be postponed until the new member has joined and another vote can be held. -The `scverse` steering council may be contacted at [steering-council@scverse.org](mailto:steering-council@scverse.org). +The scverse steering council may be contacted at [steering-council@scverse.org](mailto:steering-council@scverse.org). ### Management Committee @@ -110,7 +110,7 @@ Occasionally, sensitive discussion may occur via a private message. Decisions should be made in accordance with the mission and values of the scverse project. -scverse uses a “consensus seeking” process for making decisions. +Scverse uses a “consensus seeking” process for making decisions. The group tries to find a resolution that has no open objections among relevant core team members. Core members are expected to distinguish between fundamental objections to a proposal and minor perceived flaws that they can live with, and not hold up the decision-making process for the latter. If no option can be found without objections, the decision is escalated to the SC, which will itself use consensus seeking to come to a resolution. diff --git a/content/blog/2025-07-biomni.md b/content/blog/2025-07-biomni.md index 35b851d7..ff0e2383 100644 --- a/content/blog/2025-07-biomni.md +++ b/content/blog/2025-07-biomni.md @@ -12,9 +12,9 @@ Single-cell and spatial omics have unlocked unprecedented insights into cellular Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges. While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.readthedocs.io/en/latest/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.readthedocs.io/en/latest/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities. -**scverse** is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling. +Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling. -We’re excited to announce a collaboration between **scverse** and **Biomni** to further streamline and enhance single-cell and spatial omics analyses. +We’re excited to announce a collaboration between scverse and **Biomni** to further streamline and enhance single-cell and spatial omics analyses. Biomnis intelligent agentic interface is now capable of using scverse tools, enabling researchers to seamlessly integrate, execute, and manage analyses across ten core scverse packages through natural language prompts. Researchers can describe their analysis goals in plain English - e.g., *“cluster cells and identify markers”* or *“analyze perturbation effects between treatment groups”* - and Biomni automatically generates and runs the corresponding scanpy, pertpy, squidpy, or scvi-tools code. diff --git a/content/blog/hello-world.md b/content/blog/hello-world.md index 5a2efb57..0ca322cd 100644 --- a/content/blog/hello-world.md +++ b/content/blog/hello-world.md @@ -7,7 +7,7 @@ draft = false Due to the increasing reliance of scientific research on complex computational pipelines, foundational software in the life sciences has outgrown individual labs and institutes in terms of its scale and impact. This has motivated us to start something more than a code repository for an exciting new project – a new consortium to organize and support core (mostly) Python tools for single cell life science research. -We are excited to announce **scverse**. +We are excited to announce scverse. ## What tools are part of scverse? @@ -33,7 +33,7 @@ to help them to jump-start their new libraries. ## Who is a part of scverse? -**scverse** is explicitly an effort beyond just a single research group. +Scverse is explicitly an effort beyond just a single research group. As a community effort we strive for interoperability, shared growth, and democratized governance. In our initial form, we have divided responsibilities into several [roles](/people/), including: @@ -47,5 +47,5 @@ Our management committee, consisting of [Fabian Theis](https://www.helmholtz-mun We're particularly excited about the community coming together for this effort with so many brilliant people involved who design tools, write code, manage and analyse data and visualise results. Please ask usage questions on [our Discourse forum](https://discourse.scverse.org/), developer questions on [our Zulip chat](https://scverse.zulipchat.com/) and make sure to [follow us on Twitter](https://twitter.com/scverse_team) to keep track of scverse updates. -scverse is very much open to contributions in all areas by **everyone**. +Scverse is very much open to contributions in all areas by **everyone**. We strongly believe in diversity of all kinds being a requirement and a strong benefit for a healthy community. Hence, we embrace people from all backgrounds and experiences, who challenge each other’s assumptions with fresh perspectives. We’re committed to fair treatment and access for all members of the scverse community which is reflected in our [code of conduct](https://github.com/scverse/governance/blob/main/CODE_OF_CONDUCT.md). A sense of belonging is important to us, so we strive to actively foster a community where everyone is and feels welcomed, respected, supported, and valued. We want to especially encourage people from underrepresented backgrounds to contribute and to reach out. diff --git a/content/events/_index.md b/content/events/_index.md index 29e42815..fbbad351 100644 --- a/content/events/_index.md +++ b/content/events/_index.md @@ -4,7 +4,7 @@ title: Events ## Open community meeting -scverse community meetings happen **every two weeks on Tuesday at 6pm CET** and are open to +Scverse community meetings happen **every two weeks on Tuesday at 6pm CET** and are open to everyone! If you are new to scverse, these meetings are a great way to get to know the people behind the project. diff --git a/content/people/_index.md b/content/people/_index.md index 06a83eeb..35deb8f9 100644 --- a/content/people/_index.md +++ b/content/people/_index.md @@ -6,7 +6,7 @@ preface = "For people participating in and interacting with the consortium, ther [[teams]] name = "Core Team" - text = "The Core Team is governing scverse and is deeply involved in developing and maintaining scverse packages." + text = "The Core Team is governing scverse and is deeply involved in developing and maintaining scverse packages." [[teams.members]] name = "Philipp Angerer" @@ -210,7 +210,7 @@ preface = "For people participating in and interacting with the consortium, ther [[teams]] name = "Management Committee" - text = "The Management Committee is committed to supporting scverse and is directly involved in investing in its progress." + text = "The Management Committee is committed to supporting scverse and is directly involved in investing in its progress." [[teams.members]] name = "Francesca Finotello" @@ -245,7 +245,7 @@ preface = "For people participating in and interacting with the consortium, ther [[teams]] name = "Advisory Committee" - text = "The Advisory Committee helps to shape the overall vision for scverse and to define its priorities." + text = "The Advisory Committee helps to shape the overall vision for scverse and to define its priorities." [[teams.members]] name = "Alex Wolf" @@ -306,7 +306,7 @@ preface = "For people participating in and interacting with the consortium, ther [[teams]] name = "Community" - text = "Everyone who uses scverse software is part of the community! There are multiple ways to engage with its other members. For a start, join us on our Zulip chat, our Discourse forum, and keep an eye on our X (Twitter) and Bluesky accounts for the events we organise." + text = "Everyone who uses scverse software is part of the community! There are multiple ways to engage with its other members. For a start, join us on our Zulip chat, our Discourse forum, and keep an eye on our X (Twitter) and Bluesky accounts for the events we organise." [[teams]] name = "Single cell & Spatial Proteomics Working Group" @@ -374,7 +374,7 @@ preface = "For people participating in and interacting with the consortium, ther [contributors] name = "Contributors" - text = "All this work makes sense only in the context of the larger community of contributors and users of scverse projects. Open-source scverse projects are open to contributions, and all these people have contributed to our community (ranked by number of GitHub contributions)." + text = "All this work makes sense only in the context of the larger community of contributors and users of scverse projects. Open-source scverse projects are open to contributions, and all these people have contributed to our community (ranked by number of GitHub contributions)." +++