[Mandarin workshop]: Visualization and exploration of MSAs and associated data with ggmsa

[nyzhoulang]

Abstract

The stacked alignment graphic that represents all individual sequences as rows and homologous residue positions as columns is used almost universally in the visualization of multiple sequence alignment (MSA). We present the R package ggmsa to extend MSA visualization method via integrating stacked MSAs and associated data. Sequence-related data sets such as secondary structures, genes locus, or phenotype are allowed to combining with MSA for exploring the sequence-structure-function relationship. And we developed and integrated multiple alignment visualization methods such as nucleotide difference plots, nucleotide similarity plots, and sequence bundles to exploring multifaceted sequence features from multiple perspectives. The ggmsa package is available at https://github.com/YuLab-SMU/ggmsa.

The workshop will be organized into three broad sections:

1. Visualization of MSAs and annotations via Grammar of Graphics
2. Integration of stacked MSAs plot and associated data.
3. Exploration of sequence features via different sequence visualization methods

Language used in the workshop

Mandarin

Convenient day for your Long workshop.

No response

Contact Details

nyzhoualng@gmail.com

Comment field

No response

Checklist

• This workshop has a Bioconductor focus or interest to Bioconductor users/developers.
• I checked and confirmed the BioC Asia 2021 Code of Conduct.
• I understood that it would be desirable for the workshop to be based on this template project.

[kozo2]

@nyzhoulang Thank you for submitting this abstract.
I will contact you again on October 8th (Hawaii time).

[kozo2]

@nyzhoulang Thank you for the abstract.
I accepted it.
You can see the schedule at https://biocasia2021.bioconductor.org/workshops/ .
We will have the workshop on Zoom "Meeting".
I will contact you later about the Zoom "Meeting".

Thank you again.

[kozo2]

@nyzhoulang Can I ask you to give me your name and abstract also in Mandarin?

[nyzhoulang]

Hi, @kozo2
Here is my name and abstract in Mandarin. Thank you!

Name: 周烺 (Lang Chau)
Abstract:
在多序列比对(Multiple Sequence Alignment, MSA)的可视化中，普遍采用堆叠可视化的形式，其以行表示每条序列，以列表示相同位置的不同残基字符。我们开发的R包ggmsa在可视化层面扩展了这种堆叠形式的可视化方法，使得MSA图形可以与各类数据进行整合。例如：允许将序列二级结构信息、基因座位点信息或表型数据等序列相关的数据集与MSA结合，以此来探索序列-结构-功能三者之间的关系。并且，我们还开发和整合多种特别的比对序列可视化方法，包核苷酸差异图、核苷酸相似性图 (鉴定序列重组信号)、序列集束(Sequence Bundles)和序列标识(Sequence Logos)，这允许用户从不同角度探索序列的特征。ggmsa可以在git:上找到https://github.com/YuLab-SMU/ggmsa

Workshop将分为三个部分:
1.使用图形语法对MSA进行可视化和注释。
2. 整合MSA图形和其他数据。
3. 通过其他序列可视化方法探索序列特征。

[kozo2]

Thanks @nyzhoulang
I added the Mandarin information to your workshop.
https://biocasia2021.bioconductor.org/workshops/

[kozo2]

Hi @nyzhoulang ,
How is your workshop material going?
It needs to be created from https://github.com/seandavi/BuildABiocWorkshop .
Please ask me if you need any assistance.

[nyzhoulang]

Hi @nyzhoulang , How is your workshop material going? It needs to be created from https://github.com/seandavi/BuildABiocWorkshop . Please ask me if you need any assistance.

Thanks the reminder @kozo2 .
I have tried to create my workshop material ggmsaBioWorkshop2021 by this template;
but this approach encounters two problems.

1. Error: Failed to install 'unknown package' from GitHub
I getting this error on my github actions.

Fortunately, I found this fix to solve my issue. Adding an environment variable GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} into .github/workflows/basic_checks.yaml

2. Push to docker fails with denied: requested access to the resource is denied
This issue continues to haunt me.
I set the same as github secrets for DOCKER_USERNAME and DOCKER_PASSWORD.
As a precaution, I rotated secrets keys and tried again. Same outcome.
And I switched to uses: docker/build-push-action@v2 instead of uses: docker/build-push-action@v according to this fix.
It did not solve the issue for me though.

I'm not sure that it means my secrets are wrong?
Thanks,
Lang

[kozo2]

Hi @nyzhoulang
I'm checking if my Docker credentials have the same problem.
https://github.com/kozo2/ggmsaBioWorkshop2021/runs/3947369280?check_suite_focus=true
Give me a minute

[kozo2]

Hi @nyzhoulang
I cloned your repo and just changed your basic_checks.yaml repo-name: nyzhoulang/ggmsabioworkshop2021 to repo-name: kozo2/ggmsabioworkshop2021
and the Actions (pushing the image to DockerHub) worked well.

• https://github.com/kozo2/ggmsaBioWorkshop2021/runs/3947369280?check_suite_focus=true
• https://hub.docker.com/r/kozo2/ggmsabioworkshop2021

I think it means that your github secret is likely not set up well.
Can you check the contents of the attached screenshot in your https://github.com/nyzhoulang/ggmsaBioWorkshop2021 ?

[XueyiDong]

1. Error: Failed to install 'unknown package' from GitHub I getting this error on my github actions. Fortunately, I found this fix to solve my issue. Adding an environment variable GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} into .github/workflows/basic_checks.yaml

I've also met the first issue previously, and fixed it by the same way.

@seandavi Sorry to bother you here, but would it be possible to update the template to avoid this issue, which could be beneficial for future users?

[nyzhoulang]

I think it means that your github secret is likely not set up well.

Thanks, @kozo2
It is indeed I have a wrong secret and everything started working well.
Thanks a lot anyway!

[kozo2]

@nyzhoulang Great. Then I will ask Sean Davis to add your workshop Docker image to Orchestra. (by email. Of course, I will also send you an email with cc. )
Give me a minute.

[nyzhoulang]

OK.
And I have a minor issue. Could I continue to edit README and vignettes on my workshop in the future?

[kozo2]

@nyzhoulang Yes, you can keep updating them.
Apparently Orchestra runs docker pull every time to launch.
We should be able to get the latest resources in Orchestra without having to tell Sean the update.

[nyzhoulang]

Right, thanks your assistance. @kozo2

[kozo2]

@nyzhoulang If you get errors like the attached image in the RStudio in your workshop Orchestra, uncheck the checkbox in the another attached image. The errors seem to come out when non-English is included in Rmd.

[nyzhoulang]

uncheck the checkbox in the another attached image. The errors seem to come out when non-English is included in Rmd.

Nice~（｡ò ∀ ó｡）
Thanks anyway！@kozo2

[nyzhoulang]

Hi, @kozo2
Sorry to bother you again.
The basic_checks.yaml does not work properly after the Bioconductor released version 3.14
It seem to be a version conflict?

[kozo2]

@nyzhoulang Sorry for my late reply.
I send a pull request to fix the error now.

[kozo2]

@nyzhoulang This is bacause Bioconductor released new version recently.
And the Docker image is also updated.
I think you need to replace the bioconductor/bioconductor_docker:devel to bioconductor_docker:RELEASE_3_14

[kozo2]

@nyzhoulang basic_checks.yaml and Dockerfile have the bioconductor/bioconductor_docker:devel. So if you replace it to bioconductor_docker:RELEASE_3_14, everything goes well. (I hope so...)

[kozo2]

@nyzhoulang Thanks, I checked you already updated the basic_checks.yaml and Dockerfile (before I send a PR).
It seems the update fix the error you met. https://github.com/kozo2/ggmsaBioWorkshop2021/runs/4100384251?check_suite_focus=true

[nyzhoulang]

Thanks @kozo2 ,
Yeah! I fixed it as soon as you sent me the first message.
Thanks your attention!