#biocwebsite

2021-04-29

Kozo Nishida (12:35:54): > @Kozo Nishida has joined the channel

Kozo Nishida (12:35:54): > set the channel description: Talk about renewal plan of bioconductor.org

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Hervé Pagès (16:53:08): > First item on the TODO list: fix DNA helix in Bioconductor logo:wink:

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2021-04-30

Luke Zappia (02:36:18): > @Luke Zappia has joined the channel

Kevin Rue-Albrecht (06:30:03) (in thread): > ahhh i only fixed it in the sticker I guess

2021-05-01

Jim Hunter (06:50:02): > @Jim Hunter has joined the channel

2021-05-02

Kozo Nishida (10:23:45): > I would like to add Kaggle like user page tobioconductor.org. > (Seehttps://www.kaggle.com/rtatman) > And on the user page, I would like to show their performance tiers of contribution to the Bioconductor community with BiocBadge based on thehttps://kevinrue.github.io/BiocChallenges/package. > I would like to call this BiocIdentity. > Let me know if anyone has any ideas for implementing this. - Attachment (kaggle.com): Rachael Tatman | Kaggle > Kaggle is the world’s largest data science community with powerful tools and resources to help you achieve your data science goals. - Attachment (kevinrue.github.io): Challenges for the Bioconductor community > This package hosts challenges contributed by and for the Bioconductor community. It provides functionality to manage, filter, and display challenges as articles of a pkgdown website. Challenges are bite-sized projects led by volunteers, encouraging collaboration and sharing of expertise between contributors.

Kozo Nishida (10:31:41): > Also, likekaggle.comorpaperswithcode.com, I would like to organize the information contained inbioconductor.orgby dataset or methods. > (Seehttps://paperswithcode.com/datasets,https://paperswithcode.com/methods,https://www.kaggle.com/datasets,https://www.kaggle.com/code) > > Let me know if you have any idea for the technology and human resources required to implement these. - Attachment (paperswithcode.com): Papers with Code - Machine Learning Datasets > 3699 datasets • 45317 papers with code. - Attachment (paperswithcode.com): Papers with Code - The Methods Corpus > 1091 methods • 45317 papers with code. - Attachment (kaggle.com): Find Open Datasets and Machine Learning Projects | Kaggle > Download Open Datasets on 1000s of Projects + Share Projects on One Platform. Explore Popular Topics Like Government, Sports, Medicine, Fintech, Food, More. Flexible Data Ingestion. - Attachment (kaggle.com): Run Data Science & Machine Learning Code Online | Kaggle > Kaggle Notebooks are a computational environment that enables reproducible and collaborative analysis.

2021-05-03

Pablo Rodriguez (04:48:25): > @Pablo Rodriguez has joined the channel

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Marcel Ramos Pérez (13:45:18): > @Marcel Ramos Pérez has joined the channel

Marcel Ramos Pérez (13:52:02): > It would be great to have the Bioconductor Package Guidelines as a BiocStyle bookdown website withEdit on GitHubbuttons to allow for easy editing (e.g., for fixing typos, adding content) similar to what rOpenSci hashttps://devguide.ropensci.org/building.html. Advantages of bookdown are that we can have runnable example:r:code and a visible (self-generated) TOC.

Mulinge Martin (15:30:39): > @Mulinge Martin has joined the channel

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2021-05-04

Kevin Rue-Albrecht (04:38:43): > I’ve just created thishttps://docs.google.com/document/d/1wjfj86dtX9tnr2E6dInxxWP5AxRaCpB6YH7kFrkqaMc/edit?usp=sharingI’ll start transferring stuff from this channel to the doc, but please do feel free to add new items or stuff that I missed - File (Google Docs): New Bioconductor Website - Specifications

Kevin Rue-Albrecht (05:13:19) (in thread): > Also, let me know if there’s a shared “Bioconductor” Google drive in which this document could live, rather than my own Drive, if it can make the document more stable.

Aedin Culhane (19:09:51): > list of CMS options -https://github.com/postlight/awesome-cms/blob/master/README.mdWordPress/Drupal./wagtail & Django etc. I don’t know which integrate better with current system, but someone with knowledge on this should recommend. Some web developers only do one system, so it will be important to align with the CMS that works best for functionality, community building and long-term maintenance of the site

2021-05-05

Kevin Rue-Albrecht (04:20:37) (in thread): > I only recognize Django (which I only toyed with for a few weeks, several years ago). And for some reason Joomla rings a bell too. > In the closed source options, I remember seeing tons of adds on youtube for Wix and Webflow. Not sure if that’s a good of a bad thing, I just remember it.

Kevin Rue-Albrecht (04:22:54): > I’m one of those who highly encouraged to get professional help for the website revamp (and I stand by that), but as an option to build things from scratch, I couldn’t help going down memory lane to revisit a web framework that I tinkered with a few years ago: > * http://bioconductor.meteorapp.com/(it might take a minute to display, as the free hosting plan uses “cold start” of the instance whenever someone visits) > * Code:https://github.com/kevinrue/bioconductor_website_meteor/tree/layout(branch: layout) > The first link to the live app is hosted on the free plan and doesn’t do anything else than display a home page with navigation bar links to nowhere and a search bar that isn’t connected to any server logic. > On that cloud hosting platform, the recommended pricing seems to be $0.11 / hr per GB:https://www.meteor.com/cloud#pricing-sectionI’ve Googled about self-hosting, and came out fairly confused about whether it’s possible or even encouraged. - Attachment (meteor.com): Meteor Cloud: The Only Full-Service Cloud Offering for Meteor Apps. > Meteor Cloud is the only full-service cloud offering built specifically for Meteor apps. Build, monitor and host on the only cloud solution designed with your Meteor app in mind. Get started today for Free!

Kozo Nishida (04:24:03) (in thread): > I found two websites like (paperwithcode.comorkaggle.com) and their source code. > 1. https://new.openml.org/(https://github.com/openml/openml.org) > 2. grand-challenge.org(https://github.com/comic/grand-challenge.org) > 1 uses “Flask, React, and Dash”, 2 uses Django. - Attachment (new.openml.org): OpenML > OpenML is an open platform for sharing datasets, algorithms, and experiments - to learn how to learn better, together.

Sean Davis (08:34:26): > Just a word of caution–I think it VERY important to not start a conversation about the website with platforms or development frameworks. I’d start, instead, with defining the governance and roles and responsibilities, etc. Develop a charter. Define a project manager. Then, you’ll be ready to start planning. Note that the web presence for Bioconductor is constantly evolving and is interconnected with lots of other bioconductor core values and projects, so being methodical, having an eye on sustainable processes, and governance is going to be very important.

Lori Shepherd (08:37:10): > Also – might be premature without a dedicated web designer hired (who might be knowledgable or have a preference to platforms and frameworks) – we currently don’t have the expertise to completely revamp the website or integrate a lot of advertised infrastructure or long term maintenance if it is moved away from the current structure

Kevin Rue-Albrecht (08:44:43): > Entirely agree with both, i’m just toying with web techs as a hobby. > The Google Doc linked above is a first effort to collect and organise specifications/features/functionality that the new website should preserve from the current websites (as well as those that already emerged from the recent discussions.

2021-05-06

Kevin Rue-Albrecht (04:49:47) (in thread): > Following a meeting with the CAB Package Review Working Group, I’ve set up a bookdown template here:https://github.com/kevinrue/bioc_package_guideI’ll revisit it later (enabling the “Edit on GitHub” link and so on).

Kevin Rue-Albrecht (04:51:41) (in thread): > @Johannes Rainer@Daniela CassolI can add you as contributors if you want to avoid forking the repo.

Kevin Rue-Albrecht (04:52:20) (in thread): > I’ve set up continuous integration as well, so that we should be able to safely merge PR

Kevin Rue-Albrecht (05:03:04) (in thread): > silly me; I already had a repository set up as a template xDhttps://github.com/kevinrue/BookBiocCSS

2021-05-11

Hervé Pagès (12:46:20): > The package repositories are hosted underhttps://bioconductor.org/packages/and are populated by scripts that run daily to propagate things from the build system and generate the package landing pages. This makes this part of the website different from the rest of the website in many aspects: size (it’s huge!), frequent updates (daily), update mechanism different from the rest of the website, mirrored by other organizations to provide fast internal package repos, served via Amazon CloudFront, repos for old Bioconductor versions frozen and on cold storage. It’s so different from the rest of the website that it might even be worth considering having it on its own server e.g.packages.bioconductor.org. As a plus this would allow availability even whenwww.bioconductor.orgis down (so people can still install packages). I’ve added this to Kevin’s document.

Matt Ritchie (22:25:04): > Thanks for the suggestion@Hervé Pagès, which is along the lines of what Martin Morgan put forward when I asked him about how one might re-develop the BioC website to better organise content:‘One idea is actually to think about different sub-domains, e.g., packages.bioconductor.org with largely programmatically generated content, developer.bioconductor.org with technical content, leaving bioconductor.org for actual users of the software.’What do others think of this approach?

2021-05-12

Hervé Pagès (00:40:46): > I don’t know about going as far as having a separate sub-domain for developers. The line between user- and developer-oriented content can be fuzzy. Also an important aspect of havingpackages.bioconductor.orgseparated frombioconductor.orgis that it’s run completely differently (content is generated automatically by scripts that are connected to the build system) and by different people. I put it in the same category assupport.bioconductor.orgor as Mike’s newcode.bioconductor.org. Each site is built on a different platform and run/maintained by different people. I don’t know ifdeveloper.bioconductor.orgwould need to run on a different platform thanbioconductor.org.

Lori Shepherd (07:45:11): > Guessing he was probably thinking that getting all the stuff in the Develop section right now developer resources, package guidelines, git resources, etc can be confusing for non developers and have it in a separate dedicated space would get it away from the naive users and make it easier to find strictly those resources

2021-05-13

Aedin Culhane (18:00:34): > I think we need to do a survey of the community, to have data upon which to build. Also maybe some analytics…how/when/where are people accessing the site. The site isn’t so mobile friendly (no burger:grinning:). I think we need to think of use-cases/personas/why people use the site… how do it create an easy on-ramp for new users, keep advanced users on top of new development and opportunity, introduce and highlight new packages/workflows and community opportunity.. how are we supporting an inclusive diverse world-wide community etc etc.

Aedin Culhane (18:02:12): > I think developers can also be new users… for example, some who is experienced in proteomics, might be a new user in single omics RNAseq. As the field grows, we are rarely experts in all aspects. An instructor also needs to take training courses. PIs may to train to learn new stuff etc Life-long learning… etc etc

Aedin Culhane (18:04:59): > We needs easy self-directed learning, but “badges” or certificates on completion, so people can find others who are or have recently taken the same course, so they have a peer group for help

Aedin Culhane (18:08:26): > When many of us started Bioconductor was a few PIs and the community was small. Now it is large, global but our web presence doesn’t allow users find peers or build community. It is mostly an information resource, and navigating it can be challenging for new people

Hervé Pagès (20:20:07): > Sounds like we’re heading towards acommunity.bioconductor.orgsub-domain:wink:

2021-05-18

Federico Marini (10:09:28): > Probably material for a quick fix: > on the pagehttp://bioconductor.org/developers/how-to/useDevel/, there’s a link to the Mac resources ->http://r.research.att.com/That page is currently no more in use, I guess. > It is probably to replace with a link tohttps://mac.r-project.org/ - Attachment (mac.r-project.org): R for macOS Developers > This is the home for experimental binaries and documentation related to R for macOS. To learn more about the R software or download released versions, please visit www.r-project.org.

Federico Marini (10:13:48) (in thread): > https://github.com/Bioconductor/bioconductor.org/pull/104

Lori Shepherd (10:15:33) (in thread): > Thanks for the pull request. I’ll look at merging it over later today or tomorrow

Federico Marini (10:20:59) (in thread): > I thought you had enough things to juggle with in the next days, so:wink:

2021-06-11

Davide Corso (04:49:37): > @Davide Corso has joined the channel

2021-07-13

Leonardo Collado Torres (11:26:42): > https://twitter.com/GwenaelleL_/status/1414633678311919620 - Attachment (twitter): Attachment > Dear @Bioconductor team, the link on your page https://bioconductor.org/about/ for citing Gentleman et al., 2004 seems to be dead. Here is the new one https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2004-5-10-r80.pdf

Marcel Ramos Pérez (12:04:19): > Related to this ^^ can we addEdit on GitHublinks to the new iteration of the website so that it be easier to create a PR for these? (I’ve updated the link)

Kevin Rue-Albrecht (12:05:36): > @Leonardo Collado Torres->https://github.com/Bioconductor/bioconductor.org/pull/111

2021-07-16

Nitesh Turaga (10:45:57): > @Nitesh Turaga has joined the channel

2021-08-12

Matt Ritchie (11:32:44): > I came across this font on twitter (https://twitter.com/apreshill/status/1425578069255888897) which might be worth considering in a website revamp to improve accessibility for low vision users:https://brailleinstitute.org/freefont - Attachment (twitter): Attachment > Tiny joys, but I’m liking this Atkinson Hyperlegible Sans Serif font, named after the Braille Institute founder and made for greater legibility and readability for low vision readers > > brailleinstitute.org/freefont - Attachment (Braille Institute): Download the Atkinson Hyperlegible Font | Braille Institute > A new typeface – greater legibility and readability for low vision readers Atkinson Hyperlegible font is named after Braille Institute founder, J. Robert Atkinson.  What makes it different from traditional typography design is that it focuses on letterform distinction to increase character recognition, ultimately improving readability.  We are making it free for anyone to use!

2021-08-22

Kozo Nishida (14:40:10): > I’m setting up a website for BioC Asia 2021.https://bioconductor.github.io/BiocAsia2021/How can I make this website available athttps://biocasia2021.bioconductor.org/instead of the URL above? - Attachment (bioconductor.github.io): BioC Asia 2021 > Site template made by devcows using hugo

Lori Shepherd (18:13:38) (in thread): > I can help with this.

Kozo Nishida (18:44:47) (in thread): > Thank you. I will contact you by direct message as soon as I’m ready to request the deployment. I will be able to ask it sometime this week.

2021-09-16

Henry Miller (18:35:32): > @Henry Miller has joined the channel

2021-10-14

Wolfgang Huber (10:23:32): > @Wolfgang Huber has joined the channel

2021-10-19

Chris Vanderaa (10:53:50): > @Chris Vanderaa has joined the channel

Chris Vanderaa (11:18:27): > I’m usingrenvto improve the reproducibility of my analyses through better dependency management. The package creates a file with version stamps on any package that is used within a project. I’m trying to restore the environment containing package with those stamped versions butrenvfails to retrieve the correct source url for Bioconductor packages. Let’s take the example of S4Vectors 0.31.4,renvseems to be looking for the source at either one of two urls below: > * https://bioconductor.org/packages/3.14/bioc/src/contrib/Archive/S4Vectors/S4Vectors_0.31.4.tar.gz > * https://bioconductor.org/packages/3.14/bioc/src/contrib/Archive/S4Vectors/0.31.4/S4Vectors_0.31.4.tar.gz > Opening the two links in the browser indeed lead to twoPage not foundpagesMy questions:did the website structure recently change? How are we supposed to retrieve a specific version of a package (for instance S4Vectors0.31.4)?

Kayla Interdonato (11:46:21): > @Kayla Interdonato has joined the channel

Andres Wokaty (11:47:30): > @Andres Wokaty has joined the channel

Hervé Pagès (12:02:52) (in thread): > You can’t retrieve a specific version of a devel package (e.g. S4Vectors 0.31.4), only of a release package:https://bioconductor.org/packages/3.13/bioc/src/contrib/Archive/S4Vectors/

Chris Vanderaa (12:05:28) (in thread): > Ah that’s why it doesn’t work! Thanks for the info!:pray:I’ll try to use package versions from the stable release then!

Marcel Ramos Pérez (12:06:01): > Hi Chris, for reproducibility I would suggest usingBiocManager.snapshotsoption, see?BiocManager::repositoriesfor more info.

Hervé Pagès (12:08:37) (in thread): > I should have mentioned: you can see the link “Old Source Packages for BioC 3.13” at the bottom of the package landing page in release but not in devel.

Lluís Revilla (12:09:01) (in thread): > I think it is intended. Bioconductor works with fixed release schedule so you only can access to the latest on each release (in this case 0.31.5) viahttp://bioconductor.org/packages/3.14/S4VectorsIf there are several bug fixed on each release only the latest is stored (on Bioconductor) as the releases should only contain bug fixes and not new features/addition. Probably on RSPM you might find the other versions. This might be a good issue to rise torenv - Attachment (Bioconductor): S4Vectors (development version) > The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Chris Vanderaa (12:30:33) (in thread): > Thanks for the comments !:pray:For the context, I am making vignettes that replicates existing analyses, but I cannot afford to maintain the vignettes up-to-date with the latest packages. > I now realize that not accessing to between-release versions could make things a little more difficult as I am constantly relying on the latest devel at the moment of the snapshot, meaning that some changes that may occur until the next release could break the code. But I guess the best practice would be to wait the next release, make sure everything still works and then take a snapshot withrenv.

Chris Vanderaa (12:33:41) (in thread): > Thanks for pointing toBiocManager.snapshots! I had not seen that. I like thatrenvallows the integration with Python (I’m usingreticulatein some analyses). Do you know if this is also supported byBiocManager?

Marcel Ramos Pérez (13:05:52) (in thread): > It only works for CRAN and Bioconductor package versions

Vince Carey (13:55:40) (in thread): > to get reproducible integration with python consider bioconductor’s basilisk, in which one pins the versions of all the required python modules when creating the environment for interoperation

2021-10-20

Chris Vanderaa (02:23:36) (in thread): > Thanks!

2021-10-28

Jenny Drnevich (11:49:19): > I hope this is the right place to leave feedback on the website… We are in the weird fall state where two different Bioc versions are available for R 4.1. Onhttps://bioconductor.org/install/, the “Upgrading installedBioconductorpackages” section seems to address this and says: > “Some versions of R support more than one version ofBioconductor. To use the latest version ofBioconductorfor your version of R, enter:” > > if (!requireNamespace("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() > > However, following the above does not check or ask about using 3.14 vs. my current 3.13: > > > if (!requireNamespace("BiocManager", quietly = TRUE)) > + install.packages("BiocManager") > > BiocManager::install() > 'getOption("repos")' replaces Bioconductor standard repositories, see > '?repositories' for details > > replacement repositories: > CRAN:[https://cran.rstudio.com/](https://cran.rstudio.com/)Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) > Installation paths not writeable, unable to update packages > path: C:/Program Files/R/R-4.1.1/library > packages: > lattice, mgcv, nlme, survival > Old packages: 'AnnotationForge', 'AnnotationHub', 'arm', 'backports', 'bslib', > 'cli', 'clue', 'colourpicker', 'CoreGx', 'curatedMetagenomicData', > 'datawizard', 'deldir', 'dendextend', 'diffobj', 'dittoSeq', 'DOSE', > 'emmeans', 'enrichplot', 'exactRankTests', 'genefilter', 'generics', > 'goftest', 'heatmaply', 'Hmisc', 'htmlTable', 'igraph', 'insight', 'knitr', > 'lubridate', 'mvtnorm', 'performance', 'pillar', 'pkgload', 'plotly', > 'raster', 'rbibutils', 'RcppArmadillo', 'relations', 'remotes', 'rlang', > 'robust', 'rvcheck', 'rvest', 'S4Vectors', 'seriation', 'sets', 'Seurat', > 'sf', 'shiny', 'shinydashboard', 'sitmo', 'snow', 'spatstat.geom', 'spData', > 'stringi', 'svMisc', 'systemfonts', 'TCGAbiolinks', 'testthat', 'textshaping', > 'tibble', 'TSP', 'tzdb', 'usethis', 'uuid', 'viridis', 'visNetwork', 'xfun', > 'yulab.utils' > Update all/some/none? [a/s/n]: > n > > It’s only when I explicitly load the BiocManager package that it checks and suggests the newer version: > > > library(BiocManager) > Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) > Bioconductor version '3.13' is out-of-date; the current release version > '3.14' is available with R version '4.1'; see[https://bioconductor.org/install](https://bioconductor.org/install) > > Maybe slightly modify the website to show this?

Hervé Pagès (12:28:44): > Makes sense. More generally speaking I wonder if we shouldn’t replace > > if (!requireNamespace("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() > > with more idiomatic/less esoteric > > if (!require("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() > > Isn’t the standard practice tolibrary()/require()a package before using it?

2021-10-29

Marcel Ramos Pérez (15:16:45): > Hi Jenny, all R versions support two Bioconductor versions but there’s only one current release of Bioconductor for that R version. The documentation here is referring to the current release of Bioconductor / R version rather than the old release which also used R 4.1. We could change thatrequireNamespacecall torequireso that anyone on the old release also gets the message that ‘3.13’ is out of date as Hervé suggested.

2021-11-01

Jenny Drnevich (09:33:46): > Yes,requiredoes seem to be better in that it gives the warning: > > > if (!require("BiocManager", quietly = TRUE)) > + install.packages("BiocManager") > Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) > Bioconductor version '3.13' is out-of-date; the current release > version '3.14' is available with R version '4.1'; see[https://bioconductor.org/install](https://bioconductor.org/install) >

2021-12-01

Chris Vanderaa (06:11:59): > @Chris Vanderaa has left the channel

2022-03-04

Luke Zappia (09:22:03): > I think something is up with the “In Bioconductor since…” badges. They all seem to be saying 1 year, see****{limma}****for example - File (PNG): Screen Shot 2022-03-04 at 15.20.47.png

Lori Shepherd (09:43:07): > thanks I’ll look into it

2022-03-05

Kevin Rue-Albrecht (07:07:35): > #ForeverYoung:smile:

2022-03-10

Lori Shepherd (10:50:47): > This should be fixed and reflected on the landing pages over the next day or so

2022-03-11

Leonardo Collado Torres (17:17:20): > ahh, thanks for catching this Luke! I was looking athttp://bioconductor.org/packages/qpcrNorm/and was completely confused as to why a 2009 paperhttps://doi.org/10.1186/1471-2105-10-110would talk about a package that only had been in BioC for 1 year or less. We were speculating that maybe passing all the BioC checks took them a long time:stuck_out_tongue:Thanks for the quick fix Lori! - Attachment (Bioconductor): qpcrNorm > The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. - Attachment (BioMed Central): Data-driven normalization strategies for high-throughput quantitative RT-PCR - BMC Bioinformatics > Background High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage technology allows the acquisition of profiles for a moderate number of genes (50 to a few thousand), and this number continues to grow. The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline. Results We present and evaluate two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches. We evaluated the performance of these methods against a single gene housekeeping gene method and our results suggest that quantile normalization performs best. These methods are implemented in freely-available software as an R package qpcrNorm distributed through the Bioconductor project. Conclusion The utility of the approaches that we describe can be demonstrated most clearly in situations where standard housekeeping genes are regulated by some experimental condition. For large qPCR-based data sets, our approaches represent robust, data-driven strategies for normalization.

2022-05-05

Lori Shepherd (10:45:42): > :warning:The search onbioconductor.orgis currently unavailable. we are investigating the issue.

2022-09-12

Samuel Gamboa (13:31:51): > @Samuel Gamboa has joined the channel

2022-09-26

Henrik Bengtsson (19:28:32): > @Henrik Bengtsson has joined the channel

Henrik Bengtsson (19:28:55): > FYI, the SSL certificate forhttps://code.bioconductor.org/expired two days ago (on 2022-09-24)

Lori Shepherd (21:35:39): > @Mike Smithcan you update? I did all the other certificates a week or two ago

2022-09-27

Vince Carey (07:51:52): > I’ve been wondering about ways to make the website have more of a “need to check it out today” character.https://vjcitn.shinyapps.io/carodemo/is a very rudimentary approach to selectable carousel based on slickR. The idea is that the visitor chooses a track like methods, blogs, feeds and curated “slides” and links are presented in carousel format. Thus choices in carodemo are arbitrary, i hope they are all fair use … and the twitter feed iframes are too constrained … code is app.R athttps://github.com/vjcitn/bcpicsand PRs/issues are welcome. If this were deemed useful, an approach to eliciting diagrams and blurbs from package/methods authors would be formalized, along with some kind of curation process for other types of content. One could imagine tracks with different topical specialties; ultimately the attraction is convenient access to bioc-oriented slices of the twittersphere, blogosphere, etc.

Henrik Bengtsson (17:11:21) (in thread): > ~Has been resolved (verified on 2022-09-27)~Woops. Wong. It was only in my browser where I allowed it temporarily

2022-09-29

Mike Smith (05:42:19) (in thread): > Thanks@Lori ShepherdThis should now be sorted.

Henrik Bengtsson (18:58:22) (in thread): > Confirming. Thx

2022-10-07

Maria Doyle (09:47:50): > @Maria Doyle has joined the channel

2022-10-12

Janani Ravi (12:33:57): > @Janani Ravi has joined the channel

Maria Doyle (12:55:14): > Website working groupto create initial list of requirements (if you’re interested in joining contact me). Proposing monthly meeting 3rd Thursday of the month please vote > 9am ET:green_heart:or 12pm ET:yellow_heart: - Attachment (workinggroups.bioconductor.org): Chapter 2 Currently Active Working Groups / Committees | Bioconductor Working Groups: Guidelines and activities > The following describe currently active working groups listed in alphabetical order. If you are interested in becoming involved with one of these groups please contact the group leader(s). 2.1…

2022-11-03

Luke Zappia (04:24:17): > I think there is a bug on the release notes page where the the formatting for everything after RTCGAToolbox is messed up (there is just a big chunk of un-rendered markup). Maybe there is a tag which isn’t closed properly at the end of RTCGAToolbox?

Lori Shepherd (07:39:12) (in thread): > yikes! thanks for pointing it out – I’ll get on correctnig right away!

Leonardo Collado Torres (10:30:45) (in thread): > Thanks to both of you! > > This might be related, but well, do you know why this happened? I know thatBiocPkgToolsuses aNEWSfile whereas atbiocthisI use aNEWS.mdfile. Dunno if that’s why one is marked up and the other isn’t. - File (PNG): Screenshot 2022-11-03 at 10.30.02 AM.png

Leonardo Collado Torres (10:31:26) (in thread): > Compare the markup in the previous screenshot vs the one belowhttps://github.com/lcolladotor/biocthis/blob/master/NEWS.md - File (PNG): Screenshot 2022-11-03 at 10.31.20 AM.png

Lori Shepherd (10:32:42) (in thread): > NEWS , NEWS.md (and the less popular NEWS.rd) are still all valid formats of NEWS files per R standard – and Bioconductor does not force one over another (at least right now) – And yes it causes slightly different rendering

Lori Shepherd (10:33:23) (in thread): > The cause was the email included in the news file was surrounded by the special character <> and it would not render

Lori Shepherd (10:34:46) (in thread): > I removed the <> and the announcement now renders properly

Marcel Ramos Pérez (10:59:45) (in thread): > How do these get rendered? I didn’t expect this formatting fromBiocPkgTools:stuck_out_tongue:being that it is a plainNEWSfile as Leo said, where as it’d be nice to see this format forNEWS.mdfiles too

Marcel Ramos Pérez (11:00:56) (in thread): > FWIWutils::news(package = "BiocPkgTools", Version == "1.16.0")does not show this rendering

Maria Doyle (11:30:48) (in thread): > To update, organised for 3rd Thursday of month 1pm ET in Nov, Dec & Jan

Hervé Pagès (14:25:15) (in thread): > IIRCgetPackageNEWS/printNEWSfrom thebiocViewspackage are used for this. Lots of stuff that doesn’t have much to do with views has piled up there over the years. Maybe time to revisit.

Henrik Bengtsson (16:32:19): > It looks like thedevelpackage landing pages (e.g.https://bioconductor.org/packages/devel/bioc/html/affxparser.html) don’t have NEWS links, whereas thereleasepages (e.g.https://bioconductor.org/packages/release/bioc/html/affxparser.html) do

Hervé Pagès (17:30:26) (in thread): > Even though the file is actually there (https://bioconductor.org/packages/devel/bioc/news/affxparser/NEWS), interestingly.

Lori Shepherd (18:10:25) (in thread): > I’ll look into it

2022-11-05

Henrik Bengtsson (13:22:33) (in thread): > It’s not just NEWS - vignettes are also missing, e.g.https://bioconductor.org/packages/release/bioc/html/AlpsNMR.htmlvshttps://bioconductor.org/packages/devel/bioc/html/AlpsNMR.htmlfrom devel pages

Lori Shepherd (17:52:00) (in thread): > I’ll check on Monday.

2022-11-07

Lori Shepherd (08:46:13) (in thread): > It looks like this has resolved itself

Lori Shepherd (08:46:44) (in thread): > If you still can’t see the NEWS / vignettes I suggest resetting your browser cache / cookies for the Bioconductor site

Henrik Bengtsson (11:03:43) (in thread): > Thanks. Yes, I noticed that too yesterday. > > PS. The reason why it’s still not there for the devel version of AlpsNMR is probably because AlpsNMR now fails its checks (which in turn is becausehttps://github.com/YuLab-SMU/ggtree/issues/541whose fix is about to roll out)

Lori Shepherd (11:08:09) (in thread): > yes if it hasn’t built yet at all on teh builders than it wouldn’t have the renders vignette to show

2022-11-17

Alex Mahmoud (13:11:58): > @Alex Mahmoud has joined the channel

2022-11-21

Maria Doyle (06:00:48): > We have a new channel#social-mediafor Bioconductor social media discussions (Blog, Twitter, Mastodon, LinkedIn, YouTube, Bilibili, WeChat, Weibo etc) that anyone is welcome to join.

2022-11-23

Kevin Rue-Albrecht (12:28:29): > I thought Software/AnnotationData/ExperimentData/Workflow were mutually exclusive? - File (PNG): image.png - File (PNG): image.png

Marcel Ramos Pérez (12:32:38) (in thread): > It looks like it is only in Bioc as a software package and not in annotation > > "AgiMicroRna" %in% rownames(available.packages(repos = BiocManager::repositories()["BioCann"])) >

Kevin Rue-Albrecht (12:33:22) (in thread): > Thanks I didn’t think to check further. I fetched the information in the screenshot from BiocPkgTools, not sure where itself gets it from

Marcel Ramos Pérez (12:34:46) (in thread): > The DESC file has these entrieshttps://code.bioconductor.org/browse/AgiMicroRna/blob/master/DESCRIPTIONI’m not sure if any are in theAnnotationDatatree

Kevin Rue-Albrecht (12:35:34) (in thread): > Ah, I see thatAgilentChipis underAnnotationData

Kevin Rue-Albrecht (12:36:27) (in thread): > that’s where it pulls it from then

Marcel Ramos Pérez (12:36:52) (in thread): > EitherbiocViewsorBiocCheckmakes sure that all the terms come from one tree, it may have slipped through. I will take a look later.

Kevin Rue-Albrecht (12:38:05) (in thread): > No worries, I was just messing about with my prototype of new website, and couldn’t have more accidentally stumbled onto that one package xD

2022-11-24

Kevin Rue-Albrecht (04:28:47) (in thread): > Well, now that I’m paying attention, I’ve also spottedagilpthat does not haveanyBiocViews:wink:https://code.bioconductor.org/browse/agilp/blob/master/DESCRIPTION - Attachment (code.bioconductor.org): Bioconductor Code: Browse > Browse the content of Bioconductor software packages.

Maria Doyle (06:28:03) (in thread): > agilpalso has an interesting DescriptionMore about what it does (maybe more than one line):simple_smile:Guessing because it was accepted a long time ago (in Bioc >10 yrs)

Kevin Rue-Albrecht (07:16:19) (in thread): > I thought so too, but much older packages likelimmaare fine. I suppose this is a combination of a package being developed outside the core team and the review process having changed over time:slightly_smiling_face:

2022-11-25

Kevin Rue-Albrecht (06:22:05): > Hi all, > In preparation for the next working group meeting on Monday (28th Nov), I thought I’d mention a prototype of Node.js website that I’ve been toying with over the past week. I hope it can help stimulate the discussion and brainstorming. > The website is live here:https://bioconductor-website-next.vercel.app/The code is here:https://github.com/kevinrue/bioconductor-website-nextI’ve opened some issues to keep track of ideas here:https://github.com/kevinrue/bioconductor-website-next/issuesFeel free to open more issues directly on the repo, or use it for inspiration in the working group’srequirementsdocument. > I look forward to the call on Monday! - Attachment (bioconductor-website-next.vercel.app): Bioconductor - Home > Work in progress by Kevin Rue-Albrecht - File (Google Docs): Website Redesign Brief

Kevin Rue-Albrecht (09:28:07): > Example of a discussion for the working group:https://github.com/kevinrue/bioconductor-website-next/issues/17 - Attachment: #17 Poll: Should the website display every version of code of conduct for every language? > In other words, should the website layout be like this: > > > code-of-conduct/ > ├── en-US/ > │ ├── 1.0.1.md > │ └── 1.0.2.md > ├── fr-FR/ > ├── 1.0.1.md > └── 1.0.2.md > > > Or should the website only display the latest version for each language, i.e. website layout like this: > > > code-of-conduct/ > ├── en-US.md > └── fr-FR.md >

2022-11-27

Shila Ghazanfar (23:37:41): > @Shila Ghazanfar has joined the channel

2022-12-02

Kevin Rue-Albrecht (06:43:19): > Hi all, > Following feedback form the latest working group meeting, I’m about to merge a PR that rewires the website tofocus on the latest release by default, leaving the option to navigate to other releases, but giving them less emphasis in the UI. Screenshot of “before” (current main branch):https://bioconductor-website-next.vercel.app/ - Attachment (bioconductor-website-next.vercel.app): Bioconductor - Home > Work in progress by Kevin Rue-Albrecht - File (PNG): image.png

Kevin Rue-Albrecht (06:45:13): > Instead, the PR replaces the prominent dropdown by a single link to/packagesthat directly takes users to the list of packages for the current releasehttps://bioconductor-website-next-jspe3nsbv-kevinrue.vercel.app/packagesI’ve added a stub of banner, for now, to visually emphasise when users are looking at the current release or any other one > Feedback welcome:slightly_smiling_face: - File (PNG): image.png

Mike Smith (10:54:56): > Are there any analytics available for the existing website? I seem to remember being a bit worried about unacknowledged Google Analytics tracking as part of the privacy working group, but I don’t see it now. I just wonder if that might help guide us to what information is most frequently sought by users, and the paths they take to navigate the existing site.

Kevin Rue-Albrecht (10:58:34) (in thread): > I saw a link in the requirements document, let me dig that up

Kevin Rue-Albrecht (11:00:03) (in thread): > https://docs.google.com/document/d/1pB69HliiHo33CPctQrBOrONudAxE3gxgzhnNhdqXbuE/edit - File (Google Docs): Website analytics

Kevin Rue-Albrecht (11:00:10) (in thread): > (linked fromhttps://docs.google.com/document/d/1qDsZeFVj1n3UzeGpTpT9_6mrBHux8-zAgh-K_1KzE2s/edit#) - File (Google Docs): Website Redesign Brief

Kevin Rue-Albrecht (11:45:36): > Quick poll:Of those who would be interested in contributing to the new website, what is your main barrier to doing so? > * Lack of time:clock1: > * Expertise:exploding_head:(e.g., web development, bioc build system) > * Unclear:thinking_face:(e.g.,whereandhow to contribute) > Please react using the emojis above, to tally feedback and get a sense of your views. > Feel free to add more emojis (do send a reply to caption what the emoji means, I’ll add them to the list above for visibility).

Kevin Rue-Albrecht (11:52:34) (in thread): > My idea being that by identifying those barriers, we could give ourselves a better chance to help each other overcome them and get more conttributors on board:slightly_smiling_face:

Kevin Rue-Albrecht (12:07:40) (in thread): > Thanks for the reactions so far. Keep them coming! I’ll use them to inform the discussion at the next meeting of the website working group (15 december)

Hervé Pagès (13:00:25) (in thread): > Looks good. Nice to see a version of the Code of Conduct in French. I can’t help but think that it’s no coincidence that the first ever translated Code of Conduct is aimed at the French audience:laughing:Hey, how about fixing the direction of the DNA double helix in the Bioconductor logo? Should be oriented like a wine corkscrew. Unless we want to make this extraterrestrial DNA our trademark:alien:

Kevin Rue-Albrecht (13:02:07) (in thread): > Haha thanks! > Lots more languages of CoC here ->https://bioconductor.github.io/bioc_coc_multilingual/And I picked up the logo from BiocStickers, thinking they had all been fixed there, so I didn’t pay attention at all. I should have known better, having fixed a few of the logos myself:slightly_smiling_face:

Kevin Rue-Albrecht (13:04:36) (in thread): > I’ve copied two languages into this prototype to make a dropdown worth it, but I haven’t bothered adding more than two until I know this prototype might be the real thing:wink:

Hervé Pagès (13:13:13) (in thread): > Yup, nice work. The Irish green theme looks good on my smartphone:+1:

Kevin Rue-Albrecht (15:35:12) (in thread): > done - just for the right handed helix, it should become the “right” website now:wink::stuck_out_tongue: - File (PNG): image.png

Kevin Rue-Albrecht (15:37:31) (in thread): > Though since I’m only using thebioconductor_logo_rgb.svglogo (https://github.com/Bioconductor/bioconductor.org/tree/master/assets/images/logo/svg) it’s the only one I’ve fixed here. I’m no expert on cmyk/grey/spot alternative formats

Hervé Pagès (15:49:42) (in thread): > This is awesome, thanks for the long due fix! I’m going to test it right now on a bottle of wine:grinning_face_with_one_large_and_one_small_eye:tchin-tchin:wine_glass:

Kevin Rue-Albrecht (16:08:05) (in thread): > There are a few glitches whichI’maware of and thatI haven’topen issues for yet.Let’ssee if youcan’tfind those or others still:P

2022-12-03

Kevin Rue-Albrecht (18:37:36) (in thread): > Thanks to the updated logo, and after another of tinkering, I finally found a shade of background green that seems (to me) compatible with all the other colours around it (logo, text, rest of page). Ifthere’sone thingI’ddefinitely outsource to a contractor,it’sthe pain of coming up with a satisfying colouring theme!:smile:

2022-12-05

Kevin Rue-Albrecht (10:38:09): > New pinned post with links to the current documents of the website working group: > * Website Requirements Document(Google Drive) - File (Google Docs): Website Redesign Brief

Frederick Tan (10:49:46) (in thread): > Don’t have permissions to view

Kevin Rue-Albrecht (10:51:42) (in thread): > Hm. Interesting, I thought that was open to all. I’ve got to check with@Maria Doylewhether only members of the working have access at the moment. But the working group itself is open to all, so this document should be too, I think

Kevin Rue-Albrecht (10:54:28) (in thread): > Yeah, it’s restricted to a set of people, which I think were the ones who joined the working group so far. Maybe we can at least open it to all for viewing (and commenting?), while keeping edit access reasonably restricted.

2022-12-06

Maria Doyle (09:58:47) (in thread): > I opened it for comments

2023-01-12

Aedin Culhane (19:42:43): > Website design /UX design of OpenTargetshttps://www.sciencedirect.com/science/article/pii/S1359644617304233?via=ihub#fig0005 - Attachment (sciencedirect.com): Designing an intuitive web application for drug discovery scientists > We discuss how we designed the Open Targets Platform (www.targetvalidation.org), an intuitive application for bench scientists working in early drug d…

Aedin Culhane (19:45:11): > Recommend we create a profile persona of a person coming to the Bioc website (this is the Open Targets person) - File (PNG): image.png

2023-03-04

Vince Carey (12:49:05): > There is a package on CRAN called shinyMobile that helps create apps that can be useful on mobile devices. This could be useful for a bioconductor app. I would love to be able to click on an icon on my phone and be able to see the bioc events calendar, for example. If anyone one the website group has time to look into this please reach out.

2023-03-07

Patricia Brianna (04:44:00): > @Patricia Brianna has joined the channel

2023-03-08

Kozo Nishida (03:52:07): > (This is just a thought) > How about adding a button like “Read it later (Pocket)” like button on each package page on the new website? > I thought that would be a good indicator of attention outside of the ranks, and it would also be useful to look back at what packages you (and I) have focused on in the past.

2023-03-22

Maria Doyle (16:05:13): > The website working group have identified a potential contractor for thewebsite redesign. > We’ll be meeting with them,NearForm, April 3rd . If you’d like to join the meeting let me know and I can send the details.

2023-04-03

Vince Carey (11:31:15): > I will try to join the meeting at 1145 edt, please proceed without me

2023-04-05

Luke Zappia (07:29:06): > Could the source control docs page be updated to reflect that the default branch has changedhttps://bioconductor.org/developers/how-to/git/? Might also be good to add a link to the post explaining the change.

Lori Shepherd (07:38:43): > yes sorry we forgot about that page since all the material there links to and has been moved tohttp://contributions.bioconductor.org/git-version-control.html - Attachment (contributions.bioconductor.org): Chapter 21 Git Version Control | Bioconductor Packages: Development, Maintenance, and Peer Review > The Bioconductor project is maintained in a Git source control system. Package maintainers update their packages by pushing changes to their git repositories. This chapter contains several…

Lori Shepherd (07:39:41): > the link I just provided should be the main source for information so I’m not in favor of adding more to this page – we were trying to separate out package development/developer information from newbie user information

Luke Zappia (08:01:45) (in thread): > If it’s not going to be updated maybe the content should just be replaced with a link to the new docs? This is the first thing that comes up if you search “Bioconductor git” so I think a lot of people could end up looking there.

Lori Shepherd (08:03:49) (in thread): > fair point. I think replacing all the old links with the link to the the new page is appropriate – I will look at this update in the next day or two

Lori Shepherd (11:32:30) (in thread): > pushing up now

2023-06-12

Kasper D. Hansen (08:10:36): > @Kasper D. Hansen has joined the channel

Michael Love (09:05:44): > @Michael Love has joined the channel

Michael Love (09:05:54): > Eventually I would like to make a PR to the website proposing some edits to the “Documentation” box which appears in various places, before I do that though just posting this again as a google doc summarizing some proposed edits:https://docs.google.com/document/d/1DPv6xHn18avSDLHK57iYqktFzV7LwkpOpKgF34-AHno/edit

2023-06-13

Maria Doyle (09:12:08): > Hello<!channel>:wave:We’re redesigning the Bioconductor website and we need YOUR input:index_pointing_at_the_viewer:We’ve created a survey to understand the needs of our diverse user base. Whether you’re a wet lab biologist, student, data analyst, developer, system administrator, educator, or any other role, we’d love to hear from you! > > This is your chance to shape the future ofBioconductor.org! Your experiences, challenges, and ideas will help us to enhance the website’s design and structure. > > The survey takes about 5-10 minutes and closes on Friday, June 23rd. Link:https://t.maze.co/169169456We value your time and insights. Let’s improveBioconductor.orgtogether!

2023-06-15

Aedin Culhane (07:27:15): > Please has everyone done the survey.Please.It only takes 3 mins.

Kozo Nishida (13:56:04): > Hi all, > Does the website working group plan to refer toropenci.org? > I use GitHub Issue Form to ask requests for Google Calendar additions and send PRs to reflect those requests on thebioconductor.org. > But I don’t think the current workflow is very efficient.https://ropensci.org/events/looks good compared to the current Bioconductor Calendar+Event workflow. - Attachment (ropensci.org): Events > rOpenSci events

Kozo Nishida (13:59:51): > Anyway, I will askropensci.orghow the workflow for updating their event calendar is going. > Once I find that out, I will send a feedback to the biocwebsite redesign.

2023-06-22

Maria Doyle (12:23:53): > :writing_hand:New Bioconductor blog post on the website redesign projecthttps://bioconductor.github.io/biocblog/posts/2023-06-22-website-redesign/Still time to take website survey if you haven’t already, closes tomorrow:slightly_smiling_face:Link:https://t.maze.co/169169456 - Attachment (bioconductor.github.io): Bioconductor community blog - Reimagining Bioconductor.org: The Path to Our Website Redesign > Discover the journey of Bioconductor’s website redesign project. Learn about the process, from initial planning to collaboration with NearForm as we shape the future of Bioconductor.org.

2023-06-26

Lambda Moses (18:43:45): > @Lambda Moses has joined the channel

2023-06-29

Nick Zafiropoulos (07:44:46): > @Nick Zafiropoulos has joined the channel

2023-07-25

Aedin Culhane (08:37:13): > @Mikhail Dozmorov

2023-08-02

Maria Doyle (10:31:16): > A few links with updates on theBioconductor.orgwebsite redesign project: > * Bioconductor blog post:https://blog.bioconductor.org/posts/2023-08-01-website-redesign-update/ > * NearForm blog post:https://www.nearform.com/blog/nearform-is-delighted-to-announce-were-working-with-bioconductor/ > * BioC2023 slides:https://docs.google.com/presentation/d/1E2InDxMRVOTVqYvWT6hBt0ki44mLUru1-yAnzyxw2jk/edit?usp=sharing

Maria Doyle (10:33:30): > Please give your feedback on the new design by this Sunday August 6th:bit.ly/bioc-website-feedback2:pray:

Michael Love (10:34:32) (in thread): > is it possible to push back to Sunday? i imagine lots of folks will be busy up until 8/4 catching up with colleagues etc.

Maria Doyle (13:03:52) (in thread): > Yes, good point! We’ve changed it to Sunday 6th

2023-08-03

Jacques SERIZAY (03:08:31): > @Jacques SERIZAY has joined the channel

Ritika Giri (16:00:15): > @Ritika Giri has joined the channel

2023-10-02

Lluís Revilla (06:14:03): > I see that the website has a banner to the new website:http://new.bioconductor.org/. However, on Firefox it doesn’t open (I think it might be related to not having the https certificates). I suppose this is known and will be fixed one the websites is rolled out, but perhaps might leave out data from firefox users on this beta test. - Attachment (new.bioconductor.org): Bioconductor - Home > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Maria Doyle (06:51:29) (in thread): > Thanks for notifying. It also doesn’t open for me with Chrome. ping@Lori Shepherd

Lluís Revilla (06:52:20) (in thread): > I can open it in Chrome: Version 117.0.5938.132 (Official Build) (64-bit)

Lori Shepherd (07:03:45) (in thread): > yes it is known right now that we are having trouble with the https version and currently it is only available via http.

Kevin Rue-Albrecht (07:25:29) (in thread): > I’m sure it’s all related, but for me it’s not a matter of “not opening” but rather showing the old website at the new URL - File (PNG): image.png

Lluís Revilla (07:26:38) (in thread): > Yes, to me it is the same

Lori Shepherd (07:28:15) (in thread): > yes please use http for now

2023-10-05

Andres Wokaty (14:08:26): > I want to provide feedback on the new website. Should I just post here? For example, I noticed the years in Bioconductor badge isn’t working. Should I put that here or is the ‘feedback’ more general here and specific issues belong in an issue tracker?

Lori Shepherd (14:19:35): > I havent generated the badges yet for the package landing pages – I’ll try to do that tomorrow – but yes feedback for the new site can go here

Lori Shepherd (14:20:15): > also i havent added the redirects to be able to download tar manually from the landing pages either so that will also not work currently

Hervé Pagès (14:24:59): > Could the DNA double helix fixed in the logo? It rotates in the wrong direction.

Andres Wokaty (14:36:24): > the<hr>above events on the homepage seems to create a vertical scroll. It seems to be set atwidth: 100vw, but I guess it doesn’t account for the horizontal scrollbar. This seems to be fixed with addingmax-width: 100%to the css for the<hr>.

Sean Davis (14:52:22): > I’m way behind here, but where is the repo for the new site?

Andres Wokaty (14:54:39): > In Google Chrome, the content marker for the lists on the about page gets rendered as"•"rather than a bullet point, which is how it is rendered chromium and brave. (This just might be my browser.) - File (PNG): Screenshot from 2023-10-05 14-48-24.png

Andres Wokaty (14:55:04) (in thread): > There’s a link to it on the homepage:new.bioconductor.org

Hervé Pagès (14:57:27): > The coloring scheme in the code chunks seems a little bit random:http://new.bioconductor.org/packages/release/bioc/html/AllelicImbalance.htmlE.g. function names are sometimes yellow (e.g.BiocManager::install), sometimes green (e.g.browseVignettes), and sometimes a mix of white and yellow (e.g.install.packages). I don’t know how hard it would be to make it consistent with BiocStyle but that would be nice. - Attachment (Bioconductor): AllelicImbalance > Provides a framework for allelic specific expression investigation using RNA-seq data.

Marcel Ramos Pérez (15:00:21) (in thread): > Where do you see it?

Andres Wokaty (15:02:34) (in thread): > I agree that it should be consistent to improve readability. The contrast is a little harsh for my eyes with the white background.

Marcel Ramos Pérez (15:03:17) (in thread): > Hmm I don’t see that on chromium or brave. Maybe reset the cache?

Spencer Nystrom (15:04:32) (in thread): > Are you using a custom system font?

Andres Wokaty (15:05:41) (in thread): > it’s strange that i needed to reset the cache since i hadn’t looked at the website in chrome until today.

Sean Davis (15:06:11) (in thread): > I’m also not seeing it immediately.

Marcel Ramos Pérez (15:07:56) (in thread): > I am guessing this is ithttps://github.com/Bioconductor/bioconductor.org/tree/nearform-redesign2023

Andres Wokaty (15:08:03) (in thread): > yes, that’s where it is

Sean Davis (17:25:23): > From a dev perspective, does it make sense to fork the current site repo rather than develop the new site on a branch of the current site? Someone probably thought of that already, but I thought I’d ask.

2023-10-06

Aedin Culhane (05:47:47): > When I go tohttps://new.bioconductor.org/. I see the old site

Charlotte Soneson (06:07:59) (in thread): > Maybe try with http:https://community-bioc.slack.com/archives/C020U8LU59P/p1696244625279939?thread_ts=1696241643.129839&cid=C020U8LU59P - Attachment: Attachment > yes it is known right now that we are having trouble with the https version and currently it is only available via http.

2023-10-09

Aedin Culhane (09:50:49) (in thread): > Thanks

2023-10-15

Karthik Desingu (23:49:23): > @Karthik Desingu has joined the channel

2023-10-26

Daniel Niiaziiev (15:45:29): > @Daniel Niiaziiev has joined the channel

2023-12-07

Michael Love (12:53:54): > there’s a stray period on the first bullet - File (PNG): Screenshot 2023-12-07 at 12.53.34 PM.png

Michael Love (13:00:51): > Agree on the link to funders and collaborative projects

Kasper D. Hansen (13:01:03): > Wrt. funding etc I think we should only include details that we will update and keep current

Kasper D. Hansen (13:01:21): > So for any part of the website we need some way to making sure it doesn’t get out of date

Kasper D. Hansen (13:01:57): > To me, that would be a major component of any decision to include informationm

Michael Love (13:02:04): > we could put funding in periods that correspond to the U award?

Michael Love (13:02:16): > but i think funding should be listed and should be kept up to date

Kasper D. Hansen (13:03:18): > We also need to be clear on the text here. We know of the “core” funding but there is of course a lot of implicit additional funding which support the project, and that has to be thought through as part of the text

Kasper D. Hansen (13:05:29): > Anyway, my view on funding - ignoring the question of updating it - is that it provides almost zero value to most users of the website. However, our funders may want us to do it. But apart from funder requirement, I don’t think there is any value and descrbing it on the website. So I would do the minimum we have to do

Kasper D. Hansen (13:05:54): > I mean the value of the information of where the funding comes from. Obviously the funding itself is valuable:slightly_smiling_face:

Henrik Bengtsson (13:06:15): > http://new.bioconductor.org/packages/release/BiocViews.html#___Softwaretruncates the content to the left and the right. It makes no difference if I zoom in or out - it gets truncated at the exact same location. I see this with Firefox 120.0 on Ubuntu 22.04. It’s not happening with Chrome 119.0.6045.199 on Ubuntu 22.04. I’ve disabled all add-ons/extensions. - File (PNG): Screenshot from 2023-12-07 10-03-27.png

Lori Shepherd (13:09:14): > So how do we feel about removing the code syntax highlighting all together and going back to a simple really light grey background with black text (that still should be color blind friendly because of the high contrast) – I’ve also played with indented the code in the code text to make it stand out from the regular text for distinction in my test version. - File (PNG): Screenshot from 2023-12-07 13-05-34.png

Lori Shepherd (13:09:46): > you can compare this to the current that is on thehttp://new.bioconductor.org/packages/release/bioc/html/S4Vectors.html - Attachment (Bioconductor): S4Vectors > The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Kasper D. Hansen (13:09:54): > For code this simple, syntax highlighting does not add much

Lori Shepherd (13:10:30): > yes that what I was thinking – and the other pages on the website that it affects does not add – almost detracts – and sometimes seems wrong

Kasper D. Hansen (13:10:40): > All of that black background and color just makes it more jarrign to read. For most of us, this is pieces of coide that we just mentally skip when we look at the page

Kasper D. Hansen (13:11:10): > I could imagine other parts of the website where it might help, for example in a tutorial

Kasper D. Hansen (13:11:30): > So that suggests setting it on a per-page basis

Kasper D. Hansen (13:11:41): > And disabling it for package landing pages at least

Lori Shepherd (13:12:37): > there are no code tutorials directly linked the the website except the install page where syntax highlighting was already turned off by nearform

Lori Shepherd (13:12:55): > http://new.bioconductor.org/install/ - Attachment (new.bioconductor.org): Bioconductor - Install > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Lori Shepherd (13:21:26): > I don’t want to loose track of various conversation but overall here are the topics that I’d like feedback on : > 1. Any major concerns with merging to replace the old site officially ? > 2. Having a funding page in About – list major funding initiatives? > 3. Having a collaborators page in About – list major collaborators for Bioconductor infrastructure (ie, Galaxy, Microsoft, …) > 4. Code throughout website uses dark theme with syntax highlighting that seems jarring and inconsistent/useless highlighting,. Any objection to going back to a light grey with black for code chunks with no highlighting and maybe include an indent to help identify the code chunks? (the high contrast and indenting should still be compliant with accessibility for vision impaired) > 5. The badges on the landing page are just hanging out on their own side panel. Should it go back to the old where they are an inline list under the title? > 6. I’m personally not sold on the numbers in the box on the front page “Join 1 Millon + people” / “Join 1500 + Bioconductor Developers” – to me it seems sales pitchy – I can be overruled but I’d like to potentially change these – I just don’t know to what?!

Henrik Bengtsson (13:24:51) (in thread): > I’m okay keeping it basic - highlighting can always be added later. Regarding indentation: it risks consuming precious horizontal space on small screens, so I would vote against it.

Henrik Bengtsson (13:27:01): > SUGGESTION: Add HTTPS support for thenew.bioconductor.orgURL already now; lots of browser will redirect to HTTPS by default, so it takes some skills to stay with HTTP, which is required to view the new site.

Henrik Bengtsson (13:28:28): > Q: Is the new site targeting also smaller screens such as mobile phone?

Lori Shepherd (13:28:55) (in thread): > yes annoying I know. I needed to figure out why it wasn’t as I tried to configure as such and must have left out something. I was hoping if we aren’t hesitate about merging I wouldnt have to spend the time to debug something that would only be up temporarily and short term

Lori Shepherd (13:29:46) (in thread): > it should be vastly better than the old one. It was trying to be as much as possible but there were some things that were not converted yet

Maria Doyle (13:39:56) (in thread): > I don’t know how easy that is to fix but FWIW, that was the last page to get tackled in this phase of the redesign and was tricky as it uses JQuery (and I think a JQuerytools library that’s broken). The recommendation was to replace it completely with a different interface to packages, which is what we will do if we are successful with the CZI EOSS6 funding to continue the work.

Maria Doyle (14:00:57) (in thread): > Yes, we did aim to make it as mobile responsive as possible.

Maria Doyle (14:15:45) (in thread): > Wondering if it would make it easier for you to see what you can move forward with if you make each yes/no point into a message with 2 emojis for people to vote yes or no

Lori Shepherd (14:25:35) (in thread): > yes probably a good idea

Lori Shepherd (14:28:16): > I’ll post all the above pinned items individually here – please use thumbs up for agree/move forward thumbs down for no – and then comment in a thread any comments/remarks

Lori Shepherd (14:29:25): > 1. Proceed with replacing the old/current website (bioconductor.org) with the current state of the new website (http://new.bioconductor.org)

Lori Shepherd (14:29:49): > 2. Add a Funding page off abouts section to list major grants/funding

Lori Shepherd (14:31:06): > 3. Add Collaborators page in abouts to recognize major collaborators for bioconductor infrastructure (ie. NumFocus , Galaxy (workshops), Microsoft (builders/hubs)…)

Lori Shepherd (14:31:38): > 4. Remove dark theme for code chunks and remove syntax highlighting that does not seem consistent or useful

Lori Shepherd (14:32:21): > 5. Move badges back to inline list under package title like it is now instead of this specialized side panel that wastes room

Lori Shepherd (14:33:12): > 6. Change “Join 1 million + people” / “Join 1500 + Bioconductor Developers

Lori Shepherd (14:36:44) (in thread): > See in channel below

Henrik Bengtsson (16:15:48) (in thread): > Copy that. So, here’s what I see on my Android mobile when I got tohttp://new.bioconductor.org/install/. I’m using Firefox; don’t know how to trick Chrome to stay with HTTP, so don’t know how it works there. - File (PNG): Screenshot_20231207-131207.png

Maria Doyle (17:18:38) (in thread): > Thanks Henrik. We removed the side panels from that page yesterday, which might have impacted the mobile view. We’ll work on fixing it. Appreciate the report!

2023-12-08

Luke Zappia (03:26:51): > I have a couple of minor comments/suggestions which you can completely ignore if you are past the stage of looking these things. > * The design of the highlighted item in BiocViews (and a few other places) is very jarring to me and doesn’t match the design of the rest of the site > * If the packages page is not full width all you see is the BiocViews panel, it would be good if this was collapsed or something when the layout changes as I don’t think this is what most people want to see - File (PNG): image.png - File (PNG): image.png

Laurent Gatto (05:29:18) (in thread): > Re the profile people are asked to join, do we want developers, or users? I feel that developers feels exclusive - it’s only a minority of the community that develops packages, most are users and don’t plan the develop packages when joining.

Laurent Gatto (05:30:09) (in thread): > I think we gain from being specific, i.e. replace people, but either say users and developers or, if only one, then I would vote for users.

Michael Love (08:35:34) (in thread): > @Lori Shepherdreally minor thing but the first bullet under “Learn” tab has a stray period. If you let me know where to PR I can fix these things

Lori Shepherd (08:37:51) (in thread): > https://github.com/Bioconductor/bioconductor.org/tree/nearform-redesign2023its still on the main sites repo under the branch nearform-redesign2023 – hence also why I want to merge it over to the default branch and just move on with it but for now its on that branch

Michael Love (08:38:24) (in thread): > ok i will send my first PR:slightly_smiling_face:

Michael Love (08:45:25) (in thread): > PR made - Attachment: #255 Stray period under help for Education and Training bullet

Lori Shepherd (08:46:12) (in thread): > thanks

2023-12-09

Mikhail Dozmorov (19:49:56): > @Mikhail Dozmorov has joined the channel

2023-12-12

Janani Ravi (13:19:52) (in thread): > :thumbsdown:for removing dark themes.:thumbsup:for removing inconsistent syntax highlighting

Janani Ravi (13:22:01) (in thread): > Agree with the comments above on mentioning users & developers instead of generic people. Also, a minor point: XX+ (without space before +) might be more helpful in suggesting it’s not X + Y.

2023-12-22

Maria Doyle (10:55:23): > :loudspeaker:**** New Bioconductor Website Launching January 3rd ****:star2:**** ****Our new website design is focused on being more welcoming and accessible. Preview it athttp://new.bioconductor.organd share your feedback in Slack#biocwebsiteImportant: UseHTTPfor the preview as HTTPS is not supported yet but will be active once the site goes live. Special thanks to@Sean Davisfor this clarification! - File (PNG): Website launch date notice.png

Sean Davis (11:54:04) (in thread): > To actually see the new site, be sure to usehttpand nothttps(which redirects to the current bioc website).

2023-12-23

Spencer Nystrom (07:15:37): > Minor site nits: > * “bioinformatic solutions” sounds off to me > * “Bioconductor in the AnVIL” everywhere else that refers to AnVIL just calls it “AnVIL” (not “the AnVIL”)

Spencer Nystrom (07:17:14): > * The “Developers” tab on the frontpage needs some extra padding (a pixel or two) at the bottom. At least on mobile it drags the edge at the bottom. - File (PNG): Screenshot_20231223-071652.png

Spencer Nystrom (07:27:18): > Also, I guess this is not exactly related, but I noticed the use of the:rsymbol:glyph in place of R frequently throughout the docs. (ex “R code” becomes “:r:code”). Is there a reason for doing that beyond “it is possible to do”? It is certainly a nonstandard choice, and I’m not sure it helps clarity (or searchability).

Maria Doyle (17:59:13): > Heya Spencer, > > Thanks for pointing these out! > 1. Language & Naming: “bioinformatic solutions” and “AnVIL” - duly noted. > 2. UI/UX: That padding issue on the Developers tab - we’ll have a look. > 3. Symbols in Docs: The “:rsymbol:” - it’s on the radar for review. > Your feedback is really helpful as we approach our Jan 3rd launch. Lori will be considering all suggestions, with some reviews possibly happening post-launch. Keep the feedback coming, and remember this channel is your go-to for any further thoughts, even after we’re live. > > Happy holidays!:christmas_tree:

Maria Doyle (18:08:22) (in thread): > Thanks for the feedback! The BiocViews highlight has recently shifted from purple to a new blue/green scheme. Curious to hear your thoughts on this change? > Also, for the BiocViews panel layout on the Packages page, check out this discussion:https://community-bioc.slack.com/archives/C020U8LU59P/p1701974396632499?thread_ts=1701972375.877169&cid=C020U8LU59P - Attachment: Attachment > I don’t know how easy that is to fix but FWIW, that was the last page to get tackled in this phase of the redesign and was tricky as it uses JQuery (and I think a JQuerytools library that’s broken). The recommendation was to replace it completely with a different interface to packages, which is what we will do if we are successful with the CZI EOSS6 funding to continue the work.

2023-12-24

Y-h. Taguchi (10:14:42): > @Y-h. Taguchi has joined the channel

2023-12-29

Manvi Yaduvanshi (09:57:08): > @Manvi Yaduvanshi has joined the channel

2024-01-02

Sonali Kumari (03:13:22): > @Sonali Kumari has joined the channel

2024-01-03

Henrik Bengtsson (14:55:50): > Congrats for going live! > > FYI, some of the button links on the front page lack Title Case. - File (PNG): image.png

Lori Shepherd (16:06:34) (in thread): > thanks pushing up a fix now should be reflected in the next hour or two

Henrik Bengtsson (22:33:15) (in thread): > Thxs for the fix. I also noticed some vertical alignment issues with links and plain text in the front-page “banner” - File (PNG): image.png

2024-01-08

Javier Carpinteyro Ponce (09:45:18): > @Javier Carpinteyro Ponce has joined the channel

2024-01-11

Saga (11:59:16): > @Saga has joined the channel

2024-01-16

Hervé Pagès (13:47:20): > I just noticed that the package landing pages for BioC 3.17 still have the big orange “development preview” banner:https://bioconductor.org/packages/3.17/Biobase - Attachment (Bioconductor): Biobase > Functions that are needed by many other packages or which replace R functions.

Lori Shepherd (13:48:53): > sorry I didnt regenerate 3.17 landing pages

Lori Shepherd (13:49:10): > I can do that later this week

2024-01-18

Lori Shepherd (11:54:20): > fixed

2024-01-19

Manvi Yaduvanshi (11:51:31): > Hey! Are there any issues related to website which I can volunteer to fix?

2024-01-22

Maria Doyle (16:31:34): > Hi Manvi, > Fantastic to hear you’re looking to chip in!:raised_hands:We don’t have issues up in GitHub yet, but there are definitely areas we could improve on the site. I’m currently coordinating with Lori on this, and we’ll have a better idea of the tasks where you could make an impact soon. I’ll reach back out to you once we have a list of items ready. Stay tuned, and thanks again for stepping up!

2024-01-25

Manvi Yaduvanshi (11:42:04): > Thankyou@Maria Doylefor the kind response, really looking forward to it. Also got my first PR merged today at Bioc , so very happy:blush:

Maria Doyle (12:21:13): > Congrats on getting your first PR merged , that’s awesome!:tada:We’re also thrilled to have you on board and can’t wait to see more of your contributions. Thanks for sharing your excitement with us!:blush:

2024-01-29

Vince Carey (10:36:05): > The design here seems in need of improvement:https://www.bioconductor.org/packages/release/BiocViews.html#___BasicWorkflow… when I visited the workflows linkhttps://www.bioconductor.org/packages/release/BiocViews.html#___Workflowit took a while for some ajax reorganization to occur. the visual layout is not appealing, lots of empty space. when you ask for a specific view it may well appear off screen - Attachment (bioconductor.org): Bioconductor - BiocViews > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. - Attachment (bioconductor.org): Bioconductor - BiocViews > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Jenny Drnevich (10:40:31) (in thread): > I’ll second this - and not just for the workflows view but everything. I have no idea what is going on technically, but the biocViews box and the package table won’t show side by side unless I zoom way out and/or make the window extremely large.

Lori Shepherd (11:13:30) (in thread): > we’ve recognized this as a needs improvement page. When we did the redesign the focus was over all navigation and usefulness esp towards beginners. I believe the next ask for funding to support improvements was to improve the search capabilities as that has also been a big ask. I believe this was going to be the next thing after search to re-evaluate and try to revamp.

2024-02-09

Sergio Oller (10:54:41): > @Sergio Oller has joined the channel

2024-02-21

Jacques SERIZAY (02:37:23): > Quick suggestion: are the core bioconductor papers (I can think at least of the 2004 paper and 2015 paper) featured anywhere in the website? there are very nice papers out there but I feel like these 2 are a must-read for newcomers to the community

Lori Shepherd (06:24:56): > https://bioconductor.org/help/publications/. We have the original technical reports listed but we could add those in with proper reference - Attachment (bioconductor.org): Bioconductor - Publications > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Maria Doyle (07:54:42): > Good suggestion Jacques. Lori’s idea to add the technical reports with references is great. The 2004 and 2015 papers are already on the About page under “Release and Core Development”, see screenshot below. But perhaps we can also move them to a more prominent spot near the About section’s start to highlight their importance for newcomers. Thoughts? - File (PNG): Screenshot 2024-02-21 at 12.44.55.png

Lori Shepherd (08:01:49): > I’ll change the publication page to highlight Bioconductor papers and initial tech reports closer to the top

Lori Shepherd (08:37:42): > the publications page will be updated in within the next hour or so

2024-03-01

Charlotte Soneson (04:55:35): > Quick question about the package short URLs (e.g.https://bioconductor.org/packages/DESeq2/) - did they use to be case-insensitive, but not anymore with the updated website? We were testing the linking from Galaxy tools to Bioc landing pages, and had the impression that the (all lower case) links that used to work now require the right capitalization. - Attachment (Bioconductor): DESeq2 > Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Maria Doyle (05:53:58) (in thread): > Not sure about the URL case sensitivity changes. Maybe@Lori Shepherdor@Hervé Pagèshave insights?

Maria Doyle (07:19:25): > :writing_hand:New Bioconductor blog post about the recent launch of the redesigned Bioconductor website. Check it out here:Bioconductor Website Update Blog Post

Lori Shepherd (07:28:40) (in thread): > As far as I am aware they have always been case sensitive. As package landing pages themselves are case sensitive and packages in R are case sensitive

Lori Shepherd (07:28:56) (in thread): > I can investigate more into it

Claire Rioualen (09:19:56): > @Claire Rioualen has joined the channel

2024-03-05

Vamika Mendiratta (02:09:22): > @Vamika Mendiratta has joined the channel

2024-03-09

Cherishma Subhasa (20:19:44): > @Cherishma Subhasa has joined the channel

2024-03-13

Janani Ravi (15:10:41): > @Maria Doyle/others: do you think it makes sense to advertise the abstract deadline (Mar 25) for BioC-US 2024 on the Bioconductor homepage to invite more applicants/registrants?

Maria Doyle (15:42:31): > Great idea Janani! I agree, it could help boost submissions and awareness.@Lori Shepherd, do you think we could feature the deadline on the homepage banner or another prominent spot?

2024-03-14

Lori Shepherd (07:53:29): > yes I’ve been meaning to ask if we wanted to change the banner at the top with website link

2024-03-17

Raihanat Adewuyi (20:42:57): > @Raihanat Adewuyi has joined the channel

2024-03-18

Hervé Pagès (14:25:01): > @Hervé Pagès has left the channel

2024-04-03

Henrik Bengtsson (15:22:51): > WISH: Make it easy to see when the next Bioconductor release is expected. It could be a rough estimate most of the time (e.g. “April/May 2024”), but when the date is set, it should show the date. Maybe in the ‘Packages’ panel on the front page - there seems to be lots of room for more information. (I just browsed/clicked around for 2 mins on the website to look for the upcoming date, but I couldn’t find it. I’m sure it’s somewhere, but it’s not obvious)

Henrik Bengtsson (15:24:49): > RELATED/PROPOSAL: Maybe provide a “gantt chart” of all Bioconductor releases can further clarify freezes, bug-fix only, and development. Something like the attached figure. - File (PNG): image.png

Henrik Bengtsson (15:28:09) (in thread): > I’m thinking this could be of interest too all Bioconductor users, not just developers. > > FWIW, the next release is given byhttps://bioconductor.org/developers/release-schedule/

Lori Shepherd (16:05:05) (in thread): > I was planning on using the banner at the top but then we added bioc2024 instead – maybe I can put both there. But yes adding to someplace else might be nice too

Henrik Bengtsson (19:17:46) (in thread): > This could probably be handled by JavaScript using Mermaid.js where the Gantt chart is described using Markdown, cf.https://mermaid.js.org/syntax/gantt.html.

Henrik Bengtsson (19:30:48) (in thread): > Yes, that could be an option. I was thinking about something like in the attached screenshot - that would reuse existing space. - File (PNG): Screenshot from 2024-04-03 16-25-22.png

2024-04-04

Lori Shepherd (08:03:16) (in thread): > added. It should propagate live in the next few hours

2024-04-10

Lori Shepherd (08:16:48) (in thread): > I did do something similar but for a single release in a keynote I did

Lori Shepherd (08:17:01) (in thread): > along with explaining why we have two branches:https://docs.google.com/presentation/d/1M7f8TkAjAAe6CDIjidtlZkdi8mSEwGsvnP9toghhVg8/edit#slide=id.gefbb2efeb4_1_473andhttps://docs.google.com/presentation/d/1M7f8TkAjAAe6CDIjidtlZkdi8mSEwGsvnP9toghhVg8/edit#slide=id.gefbb2efeb4_1_528

2024-04-15

Lluís Revilla (05:30:57): > I recently activated receiving email notifications fromsupport.bioconductor.orgfor the tags I follow to avoid missing a question tagged with my package. However, I received an email fromnoreply@bioconductor.orgto several emails (not in BCC) with links to several questions none of which are related to my tags (In addition the post are linked without the full url: “http://p/9157660/” it lacks thesupport.bioconductor.org“). I think these post are merged from all accounts that have activated the digested notification. Is there a way to improve this and receive only notifications from my tags without sending them to other people?

2024-04-16

Maria Doyle (16:24:48) (in thread): > Hi Lluís, since this issue relates specifically to the support site, it might be more effective to post it in the#support-sitechannel. Natay, who helps with troubleshooting there, might be able to provide some guidance. What do you think@Lori Shepherd?

Lluís Revilla (16:27:14) (in thread): > Oh sorry , I forgot about that channel. I’ll post there with a few other details

2024-04-20

Laurent Gatto (02:55:02): > The search on the website seems to be broken. When searching, even for a valid package name, I get “A timeout or invalid search term resulted in an error.”

Lori Shepherd (10:21:25): > Yeah its a known issue we are working on. There is an open GitHub issue for it. Sorry for the inconveniences

2024-04-21

Vince Carey (05:52:34): > can a banner be added to the website while this is down indicating how to use a google search command to search the site?

Vince Carey (05:53:44): > e.g.,site:bioconductor.orgoutliers

Lori Shepherd (11:45:25): > Sure I can add it Monday

2024-04-27

Ludwig Geistlinger (14:35:21): > It seems there are currently no 2024 download stats for experimental data packages (egairway) and annotation data packages (egorg.Hs.eg.db)?

Robert Shear (18:34:48): > @Robert Shear has joined the channel

Lori Shepherd (18:36:29): > Thanks we’ll look into it@Robert Shear

2024-05-17

Mike Smith (05:52:01): > set the channel topic: test

Mike Smith (05:52:05): > cleared channel topic

2024-06-02

Ludwig Geistlinger (16:48:55) (in thread): > Thought I quickly check back on this as the 2024 download stats for experimental data packages and annotation data packages seem to remain unavailable?

Lori Shepherd (17:02:12) (in thread): > @Robert Shear

2024-06-12

Henrik Bengtsson (22:24:39): > Banner “Registration Open for Bioc2024 Early registration discount pricing ends May 31!” should probably be updated

2024-06-13

Vince Carey (06:03:59) (in thread): > Looks like this is resolved. Is it satisfactory?

Lori Shepherd (06:06:41): > Thankyou. I’ll update this morning

Ludwig Geistlinger (06:13:30) (in thread): > Looks good to me. Thanks!

2024-06-14

Laurent Gatto (23:51:31): > I was searching for a package, Autotuner, and got a bunch of search results. When I follow the first link,https://bioconductor.org/packages/release/bioc/html/Autotuner.html, I get a ‘Page Not Found’. This makes sense, as Autotuner has been removed from Bioconductor 3.16, but the ways for my to figure this out aren’t obvious for somebody that doesn’t know about package removal, i.e either directly looking athttps://bioconductor.org/about/removed-packages/, or typinghttps://bioconductor.org/packages/Autotunerthat redirects to the Removed Packages page. > Would it be possible to directly redirect to the Removed packages page when searching for one that was removed and possibly even return links to existing/old version? - Attachment (bioconductor.org): Bioconductor - Removed Packages > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. - Attachment (bioconductor.org): Bioconductor - Removed Packages > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

2024-06-17

Vince Carey (07:48:07): > This is definitely an important concern. We do have some CZI support for site search improvement IIRC. Personally at the moment I would rather have clear documentation on removal process and user options, than modifications to automate passage … just because of the complexity and other priorities.@Lori Shepherd

2024-07-11

Sathish Kumar (06:04:14): > @Sathish Kumar has joined the channel

2024-07-20

Vince Carey (13:09:36): > the left sidebar has quite a few topics but it does not scroll. to get to the bottom i had to shrink font and expand window. - File (PNG): image.png

Charlotte Soneson (13:14:00) (in thread): > For me the sidebar scrolls to the bottom once I have scrolled to the bottom of the actual page.

2024-08-19

Rema Gesaka (09:38:54): > @Rema Gesaka has joined the channel

2024-10-17

Luke Zappia (03:47:06): > The little badges with ORCIDs don’t seem to work if the authorcommentfield contains other information (like GitHub user names). See the****{splatter}****page for examplehttps://www.bioconductor.org/packages/release/bioc/html/splatter.html#since.

2024-11-14

Janani Ravi (18:57:13): > Are the adjacent red/green colors in the dashboard difficult for folks with RG colorblindness to distinguish? Should we separate them by a neutral color, in case this is an issue?https://bioconductor.org/dashboard - Attachment (bioconductor.org): Bioconductor - Dashboard > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

2024-11-15

Lluís Revilla (04:21:10) (in thread): > Related to this, what’s the difference between that dashboard andhttps://master.bioconductor.org/dashboard/? It seems like it is the same?

Lluís Revilla (04:26:16) (in thread): > In addition on thehttps://www.bioconductor.org/about/page there is no link to the dashboard on the left menu. The link to the dashboard is only on the bottom of the page under About (and on the Developers page:https://www.bioconductor.org/developers/). - File (PNG): bioc_about_bottom.png - File (PNG): Bioc_about_left_menu.png

Lluís Revilla (04:30:07): > I cannot find theworkshop.bioconductor.orgunder the Learn page (https://bioconductor.org/help/). Is it shared on some subpage, or it is not to be shared widely yet?

Lori Shepherd (07:10:26) (in thread): > it hasn’t been shared widely yet. there was a recent discussion internally if its ready for advertisement and equip to scale if sudden large demand. I expect to add it before the end of the year

Lori Shepherd (07:11:12) (in thread): > the information there seemed most relevant to developers except maybe new packages and mirror status… but we can add it elsewhere

Lori Shepherd (07:12:06) (in thread): > master.bioconductor.orgis the main instance that then is hosted on cloudfront atbioconductor.org– they are the same but the later should be used as we don’t advertise direct access to the instance

Lluís Revilla (07:47:57) (in thread): > You don’t advertise the instance but it was picked by google, and I assume other search indexes or AI bots.

Lluís Revilla (07:48:53) (in thread): > Good to know:+1:Thanks!

2024-12-28

Michael Hungbo (07:29:05): > @Michael Hungbo has joined the channel

2025-02-06

Liz Hare (11:52:55): > @Liz Hare has joined the channel

Liz Hare (11:57:06): > Hi! I’m coming back to Bioconductor after a few years away and noticing screen reader accessibility issues with the website and support forum. I posted about this on the support forum yesterday but I wasn’t sure it was the right place to talk about the website. I also didn’t find that it was possible to submit issues to the repo for the website. I’d like to know where to document these issues as I find them.

Vince Carey (11:57:45): > This is a good place.

Vince Carey (11:58:17): > alsohttps://github.com/bioconductor/bioconductor.org

2025-02-07

Maria Doyle (17:12:00) (in thread): > Hi Liz, > Sorry to hear about the accessibility issues. As Vince mentioned, please feel free to report any problems you find through theGithub repo(https://github.com/bioconductor/bioconductor.org) or in this channel. We appreciate your feedback.

2025-02-08

Liz Hare (08:15:24) (in thread): > Thank you. I will create issues on GitHub.

2025-02-11

Michael Love (20:13:17): > Accessibility feedback on the Bioconductor website:https://support.bioconductor.org/p/9161234/#9161261

Sean Davis (21:31:26): > And issue:https://github.com/Bioconductor/bioconductor.org/issues/304 - Attachment: #304 Screen reader challenges on bioconductor.org site > From the support site: > > Hi! Thanks for all the work on an organized and useful website. I’ve found biocViews like this one https://bioconductor.org/packages/release/BiocViews.html#___ExperimentData|https://bioconductor.org/packages/release/BiocViews.html#___ExperimentData produce tables that are inaccessible with a screen reader. I’ve tested on Mac with Safari and Chrome. The screen reader sees that there is a table and it produces a description of the number of rows and columns but it cannot read the contents.

Marcel Ramos Pérez (22:23:10) (in thread): > I created a PRhere. I am not too familiar with increasing accessibility for HTML tables. It would be great if someone with more experience can review or create a more appropriate PR. - Attachment: #305 add aria-labels to biocViews table, closes #304 > • add roles and scopes > > @lshep
> I was not able to test the changes in the docker container.
> That section of the website is not so easy to test perhaps because
> the data required to dynamically generate the content is not available.

Vince Carey (22:26:05) (in thread): > those changes make sense. have you been able to build the site with your changes and try out a reader? a screencast would be nice to have

2025-02-12

Marcel Ramos Pérez (13:03:05) (in thread): > No, I wasn’t able to render that part of the website with the docker container

Sean Davis (16:19:17) (in thread): > The website includes a number of dynamically-generated components, including the table(s) and tree on the packages list page. See, for example, the output of: > > curl '[https://bioconductor.org/packages/release/BiocViews.html#___Software](https://bioconductor.org/packages/release/BiocViews.html#___Software)' > > At some point, we may want to revisit those types of pages to 1) reduce technical debt, 2) decouple infrastructure, and 3) improve automation. If I recall, there is an apache server running in front of the website, so in theory, it would be possible to rewrite that part of the website as a static site (or a set of them).

2025-02-18

Liz Hare (11:29:04): > @seandavi, thanks so much for making the issue– I finally went to do it and it was already there. I commented there but briefly, I’m the screen reader user in question. There are automated ways to check accessibility but they vary in their effectiveness. I think they could give us clues. I’m sorry I’m not a frontend web expert at all– if someone could explain a little about the software generating those tables maybe I could look for a good testing application.

2025-02-19

Idowu Festus (04:48:56): > @Idowu Festus has joined the channel

2025-03-10

Jenny Drnevich (10:46:37): > Something@Tim Trichenoticed during our Training Committee meeting today. Shouldhttps://bioconductor.github.io/show something besides a 404 error?

Lori Shepherd (10:49:31) (in thread): > there is no github pages setup for the website as it is not generated that way so not sure why we would do that. wouldn’t it just get confusing with the actual website

Jenny Drnevich (10:55:52) (in thread): > I’m not sure how Tim found it - he probably manually typed it in instead of following a link. Maybe it would be nicer if it just had a redirect, but setting up github pages can be a pain and probably not worth it.

Tim Triche (11:21:05): > @Tim Triche has joined the channel

2025-03-17

Agboola Abimbola (12:35:40): > @Agboola Abimbola has joined the channel

2025-03-27

Michael Love (10:32:02): > Id like to propose elevating this page (table of R version / Bioc version links) higher in the info hierarchy > > Would a PR be a good way to start?https://www.bioconductor.org/about/release-announcements/ - Attachment (bioconductor.org): Bioconductor - Release Announcements > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Lori Shepherd (10:34:38) (in thread): > PR always welcome – what do you mean by higher in info hierarchy? If you mean in the index on the side its alphabetical currently

Michael Love (10:35:44) (in thread): > I think it would be useful that this is listed in more places

Lori Shepherd (10:36:09) (in thread): > ah excellent. yes please a PR would be great!

Michael Love (10:37:30) (in thread): > Also, I’m thinking of a new title: while it’s accurate that it’s a list of the release announcements, it is also a demonstration of this key aspect about the project. I’m frequently looking this up both from a user and developer perspective…

Lori Shepherd (10:38:37) (in thread): > yes really the info on R / Bioconductor compatibility in addition to the release announcement

Michael Love (10:43:05) (in thread): > Maybe one to two sentence blurb with link to more detail details , followed by the table so you don’t have to scroll too far to see it

2025-04-29

Michael Love (15:05:06) (in thread): > i put some more links to this page in different locations. honestly i think it is relevant for new users and developers, so i put it both in about, help and developers areashttps://github.com/Bioconductor/bioconductor.org/pull/320

2025-04-30

Lori Shepherd (07:04:53) (in thread): > merged. should be reflected in the next hour or two