Need to add all members to organizers committee, maybe we can split in groups since this year we have committees :)

• Aedin Culhane
• Anthony Federico
• Ayush Raman
• Charlotte Soneson
• Deepak Tanwar
• Erica Feick
• Frederick Boehm
• Hector Corrada Bravo
• Helena Crowell
• Lauren Hsu
• Laurent Gatto
• Lorena Pantano
• Lori Shepherd
• Levi Waldron
• Matthew McCall
• Mikhail Dozmorov
• Martin Morgan
• Nathan Sheffield
• Oriol Senan
• Peter Hickey
• Qian Liu
• Rafael Irizarry
• Ricardo de Matos Simoes
• Sean Davis
• Simone Bell
• Simina Boca
• Tom Carroll
• Venu Thatikonda
• Vincent Carey
• Zhezhen Wang
• Anthony Federio

Hi @lpantano ,

I see that the Netlify GitHub app was installed 3 days ago in the Bioconductor organization per your request, and with access to the BioC2020 repo only. Just wanted to make sure that this was intended. Do you confirm that you need Netlify for the Bioconductor/BioC2020 repo? Thanks!

H.

Hi,

Note: this issue in response to this call for proposals for BioC2020.

Initially, for BioC2020 we had sent two talk/poster proposals that the BioC2020 planning committee suggested we repurpose as a Birds of a Feather (BOF) event, which we are happy to do. Our initial ideas were: (a) a talk about CDSB and our progress so far and (b) a talk about the regutools package which was made by and submitted to Bioconductor by CDSB alumni. We have thus combined these two proposal into the following BoF format that we would adjust the time for depending on whether we were given a 45 or 60 min BoF.

• (long) Title: CDSB community: efforts to strengthen the R/Bioconductor developer community in Mexico/LatAm and results showcased by regutools
• Session structure:
  • CDSB overview: motivation behind us, efforts with NNB-UNAM and RMB, CDSB workshops (2018, 2019 and 2020 plan), results overview. That is, a talk version of https://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico and more of our story. Presented by Alejandro Reyes @areyesq89 and/or myself.
  • regutools package project: Joselyn @josschavezf, Carmina @CarBarJon and Emiliano @jemilianosf present regutools and what it does. It is their first Bioconductor package and ideally will have a pre-print by the summer. The talk would cover: motivation of package, storyline of how it was developed across multiple phases (maybe how CDSB played a role), what the package does, how it's integrated with Bioconductor, and future plans. Presented by Joselyn, Carmina and Emiliano.
  • Q/A section: this portion of the BoF session would be open to questions from the public. We would also have some questions ready for Joselyn, Carmina and Emiliano moderated by Alejandro and/or myself. Questions could include how they became interested in becoming R/Bioconductor developers, how and what resources they used to learn to do so, what they think would have helped them more, what are their future plans and their relation to Bioconductor.

A less developed version was discussed in emails where Joselyn, Carmina and Emiliano expressed their interest to participate in this BoF.

The way I see this BoF, it would allow us to:

• Present CDSB to those who haven't heard about it.
• Report on the progress we've made at CDSB over the past year, what we have in mind for 2020, and challenges ahead.
• Provide a platform for our new BioC developers to share their work and fully join the BioC community. Like a graduation of sorts.
• Inspire others to follow parts or all of our model. While we have LatAm in sight, we have a support structure in place in Mexico which we are benefiting from and thus for now will keep working from Mexico.
• Maybe some will want to come to Mexico to teach, volunteer to help in some way or another, or maybe even sponsor our workshop events.

Based on an improvised talk at BioC2019, a few people reached out to us during the rest of the conference to share tips, provide contact info, and express their interest. That's actually how we ended up recruiting someone to join our 2020 instructors group.

Best,
Leo

From organizing document. Put on main page?

Jan 9 Registration Opens
Jan 15 Call for abstracts/applications for talks, early posters, scholarships, workshops
March 3 Deadline for proposals for talks, workshops, early posters, and travel scholarships
March 24 Notification of decision
July 1 Deadline for late posters and for Birds of a Feather meetings
July 10 Notification of decision for late posters
July 10 Last day of early registration (2x fees)
July 29-31 Bioc2020 Meeting, Boston

See https://github.com/Bioconductor/BiocStickers/tree/master/events/Bioc2020 for images

Hi,

I can't seem to find at the link to the travel scholarship details that I can see that the information exists here https://github.com/Bioconductor/BioC2020/blob/master/docs/scholarships.md. Is the information in this document correct? (from the dates it seems to be)

A CSDB member just asked me about this.

Best,
Leo

The dates on these pages should be corrected:

• https://bioc2020.bioconductor.org/schedule-developer-day
• https://bioc2020.bioconductor.org/schedule-day-one
• https://bioc2020.bioconductor.org/schedule-day-two

And "Developer Day" should be renamed to "Community / Developer Day", until we come up with a better name. Any of @mdozmorov @lpantano @HelenaLC @fboehm willing to self-assign?

Notes of the workshops yet to be incorporated in the #80 pull request

• Amaretto, two submissions to be combined, GitHub repo https://github.com/broadinstitute/BioC2020Workshop_AMARETTO-Hub
  • Mohsen Nabian|The *AMARETTO software toolbox for multimodal and multiscale network biomedicine: linking diseases, drivers, targets and drugs via multi-omics, clinical, imaging and perturbation data fusion.
  • Artur Manukyan|AMARETTO-Hub: Knowledge Graph-based Embedding of Multimodal and Multiscale Network-based Biomedicine for Deciphering Complex Relationships Across Biomedical Entities

We need a way to follow progress on issues across several workshops, and even just to keep track of where issues have been filed. As an inelegant solution, I'll just post links to the issues I've filed here.

• cmirzayi/EpiForBioWorkshop2020#1
• PeteHaitch/BioC2020_DelayedArray_workshop#2
• hukai916/IntegratedChIPseqWorkshop#1
• haibol2016/ATACseqQCWorkshop#2
• LihuaJulieZhu/CRISPRseekGUIDEseqBioc2020Workshop#1
• Kayla-Morrell/CreateAPackage#2
• LieberInstitute/recountWorkshop2020#1
• aedin/PCAworkshop#1
• broadinstitute/BioC2020Workshop_AMARETTO-Hub#1 - canceled

Erika put together the following information:

Hotels near DFCI.pdf

Hello,

I'm happy to propose a BOF on the following topic

Reproducible environments for integrated computational workflows

Input/topic: A full biological analysis workflow often requires numerous software tools deployed at individual analysis steps, some of which may have conflicting software version requirements or are written in different programming languages. In the spirit of an open discussion, we would like to gather experiences and suggestions on current solutions and best practices around the use of software environments (e.g., Conda, renv, Docker, Singularity) in combination with workflow managers (e.g., Snakemake, Nextflow, cgat-core), with a specific focus on workflows that integrate tasks involving multiple programming languages in addition to R (e.g. Python, Java, Shell).

For example, challenges and considerations faced when designing and using software environments for multi-lingual pipelines on institutional high-performance computing clusters (HPCs) include:

• Reliable support for version control of packages in each language
• Tasks needing multiple programming languages to co-exist in the same environment
• Reuse/sharing of environment between projects vs. project-specific/redundant local copies of environments allowing independent management
• Size of environments (individual and combined total disk space)
• Number of distinct environments, maintenance, and responsibility
• Sharing of environments with collaborators and the wider scientific community
• Versioning of environments

Specifically, we are keen to discuss the pros and cons of individual software environment frameworks, in relation to the context in which they are intended to be used.
For instance, the motivation and design choices behind each software environment framework influences their respective capacity to support individual programming languages. Reciprocally, individual workflow managers strive to support multiple software environments frameworks, giving users a range of choices that may lead to a paradox of choice and confusion about best practices in their respective computing environment(s).

Ideally, this could develop into a community-driven review of existing frameworks for both software management and workflow management, driven by individual experiences and combined expectations from a broad range of users.
In particular, this effort could complement the recent preprint Streamlining Data-Intensive Biology With Workflow Systems - there the focus was on a broader set of best practices for the design of streamlined computational workflows.

Output: While the conversation will be kept in a very open format to enable the participation for attendees coming from diverse backgrounds and academic levels, we would like to document and structure the output of this BoF as a collaborative manuscript, reviewing existing frameworks and best practices in designing and managing reproducible software environments for use in computational workflows for scientific research.

Kevin (@kevinrue), Charlotte (@Charlie-George)

Your sponsorship will help increase diversity and representation at Bioconductor 2020 by:

• Funding travel scholarships for students and postdoctoral fellows
• Providing caregiver awards to assist in childcare or eldercare costs (new in 2020)
• Offering student diversity scholarships to increase participation of underrepresented minorities (new in 2020)
• Keeping registration costs affordable for academic participants

Three levels of sponsorship are available. Sponsors of all levels may present a poster highlighting the scientific interests of their organization in the poster sessions.

Platinum $10,000 USD.

• Poster session will be named after these donors.
• Highest recognition, using your logo, in the online and print promotional and scheduling material.
• Two invitations to attend the speaker dinner.
• Up to 8 free registrations.
• A thank-you tweet including your preferred Twitter handle.
• A table during the poster session and social hours.

Gold: $5,000 USD:

• Top recognition, using your logo, in the online and print conference promotional and scheduling material.
• Up to 5 free registrations.
• A thank-you tweet including your preferred Twitter handle.
• A table during the poster session and social hours.

Silver: $1,000 USD

• Sponsor names will be listed in the online and print promotional and scheduling material.
• Academic discount on 2 registrations.
• A thank-you tweet including your preferred Twitter handle

Need to update dates to July 29, 30-31 2020 in all pages

Will return to this when we decide on poster format this week. If we have an external site for posters we will not need to have a dedicated page at http://bioc2020.bioconductor.org/posters.

(raised by Mike Smith on slack (bioc2020-workshops channel)).
Some description of these different labels was provided in the 2018 workshop book. Could we include something similar this year, to avoid confusion?

@schifferl are you willing to design badges again? I created a logo issue at Bioconductor/BiocStickers#99.

July 20 or before. To multiple pages

Make sessions 4x10min + 15min Q&A

IMO, "Day 1", "Day 2", etc is more complicated than necessary because we will also have the platform schedule, especially since the schedule will be changing still. Perhaps just a single page, or link to a wiki at https://github.com/Bioconductor/BioC2020/wiki?

Hi Mikhail @mdozmorov and Lorena @lpantano

The Docker link in the workshops page for Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment does not agree with the DESCRIPTION file in the workshop:

https://github.com/waldronlab/MultiAssayWorkshop/blob/0501f784d83eeb236cc06e2e3bbd86bb647ea4ed/DESCRIPTION#L49

DockerImage: mr148/multiassayworkshop:latest

For some reason, the link points to waldronlab/multiassayworkshop.
Thank you for your help.
-Marcel

Email could work, also, but the website would be helpful to capture the details, to give a better big picture to presenters, and to reuse in the future if necessary.

Platinum $10,000 USD.
-Poster session will be named after these donors.
-Highest recognition, using your logo, in the online and print promotional and scheduling material.
-Two invitations to attend the speaker dinner.
-Up to 8 free registrations.
-A thank-you tweet including your preferred Twitter handle.
-A table during the poster session and social hours.

Gold: $5,000 USD:
-Top recognition, using your logo, in the online and print conference promotional and scheduling material.
-Up to 5 free registrations.
-A thank-you tweet including your preferred Twitter handle.
-A table during the poster session and social hours.

Silver: $1,000 USD
-Sponsor names will be listed in the online and print promotional and scheduling material.
-Academic discount on 2 registrations.
-A thank-you tweet including your preferred Twitter handle

The code-of-conduct probably does, but this may need input from the community advisory board.

This is a submission of a suggested topic, in the short talks category of the upcoming conference:

Creating a MiniCran repository for a very page.rank() style library method, such as described in the following blog on Revolutions Analytics site: "https://en.wikipedia.org/wiki/PageRank" , but this repo designed specifically for usage with the biometry/bipartitite package of the cran-R repo.

The code can be included on this posters site, at request. Thanks

Below are links to the submission forms.

Travel Award:
https://forms.gle/S7P27yH4NVBtyxPJ8

Talks / Posters:
https://forms.gle/rQZFjrKgdkXjR1U3A

Workshops:
https://forms.gle/tb8hQ169XFo31NsU7

See:

Some information can be moved from previous year to this page:

https://github.com/Bioconductor/BioC2020/blob/master/docs/travel-accommodations.md

Like Airport and Boston transportation

Source: https://github.com/Bioconductor/BiocStickers/tree/master/events/Bioc2020

Hello, I would like to propose a BOF on the following topic:

Input/Topic: Color is becoming an increasingly powerful data visualization tool to represent the dimensionality of our complex and rich scientific data. However, these visualizations and the patterns therein are also becoming increasingly difficult to interpret for individuals with color vision deficiency in particular, and other vision impairments in general. Color vision deficiency affects a significant percentage of the population, and leads to difficulties in perceiving patterns in multi-colored figures. In many cases, the perceived patterns; e.g. in heatmaps and reduced dimension plots, could differ between individuals with normal and color deficient vision.

Figure: An Ishihara's test where people with normal vision see the number 74, but people with color deficiency see either no pattern, or 21/81. (From Wikipedia(https://en.wikipedia.org/wiki/Ishihara_test) and an unscientific survey on slack).

Visualization tools currently provide accessibility to colorblind developers and users through the option of choosing colorblind-friendly palettes. However, if the default visualizations in our R packages are not color-blind friendly, a vast amount of our published results risk being inaccessible to individuals with color vision deficiency. One solution to address these issues is to include colorblind friendly strategies (Color Blindness: A Point of View) as a default setting in our visualizations. Several colorblind-friendly palettes exist (e.g., see R packages viridis and dittoSeq) and can be integrated into data presentation as the default option. Even with these palettes in place, it is desirable to limit the number (about 8-10 at a maximum) of colors in visualizations. To reduce the dependence on colors, one solution would be to include additional visual cues to differentiate regions (hatched areas) or cells (point shapes).
Overall, a broader discussion regarding the accessibility of our figures that is not just limited to color vision deficiencies would be greatly beneficial towards improving data accessibility.

Note: Some of the thoughts above have also been noted in the whitepaper here: https://birsbiointegration.github.io/whitePaper/

Output: We would like to identify and recommend strategies for making standard visualizations provided by Bioconductor packages more accessible to people with vision impairments, including, but not limited to:

• Incorporating colorblind-friendly color palettes as a standard recommendation/requirement in the R package submission guidelines.
• Discussing effective visualization techniques which could reduce the dependence on color as the explanatory factor in visualizations (e.g, include point shapes, hatched areas, limiting the number of colors, etc.)
• Harnessing interactive plots to enable the choice of color palettes and other visualization tweaks to the reader.
• Addressing broader accessibility with the inclusion of "accessibility captions" accompanying figures which "guide" the reader's perception of the images, and how they could be incorporated as part of standard visualization tools.

Discussion and agreement to name conference days as Day 1, 2, and 3.

This is an editable Google Docs spreadsheet with info on local child care options in Boston, curated by @aedin.

See https://bioc2019.bioconductor.org/ (and https://github.com/bioconductor/bioc2019) for an example. Look for bio and photo on the internet, reach out to speaker if it doesn't exist.

Confirmed speakers so far are:

• Rafael Irizarry (link)
• Caroline Uhler (link)

@csoneson will you help to keep this issue up-to-date as speakers are confirmed?

Hi there,

I'm happy to propose a BOF topic in response to the call you opened - https://support.bioconductor.org/p/129518/

Ten simple rules for thriving in bioinformatics research

Input/topic: In the spirit of an open discussion, we would like to gather experiences and suggestions about how it is possible as bioinformaticians/computational biologists to develop software as well our own career in the Life Sciences, with a specific focus in the fields of academia, consulting, and research service.

How can we for example improve the opportunities for recognition of our work (e.g. by being able to publish workflows and software), and encourage evaluation based on additional metrics than the “traditional” papers and citations. Or, touching another possible pain point, how can we acquire funding being mostly in the software/method development?

We started a brainstorming session in one of the open Thematic Lounge sessions during e-Rum2020 and wanted to continue the discussion in a more targeted group.

Ideally, this could develop into a “response” to the “Ten simple rules for providing effective bioinformatics research support”, recently posted on Plos Computational Biology https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007531 - there the focus was on how to build up efficient ways to provide research support, while we would like to put a spotlight on the research aspects.

Output: While the conversation will be kept in a very open format to enable the participation for attendees coming from diverse backgrounds and academic levels, we would like to document and structure the output of this BoF pretty much as a “Ten Simple Rules” collaborative manuscript.

If you would like to show your interest with a virtual raise of hands, please do so by reacting or replying to this issue!

Federico (@federicomarini), Charlotte (@csoneson ), Davide (@drisso)

https://bioc2020.bioconductor.org/caregiver-awards.html. Cross-reference to Issue #87

It is currently set as 500 on the workshops page

Do we have them, where to find?

Get rid of extra commas that are there due to empty title/url fields