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[Bioc-devel] workflow page reorganization

10 messages · Laurent Gatto, Andrzej Oleś, Shepherd, Lori +3 more

Original
Shepherd, Lori
# 
Hello all,


There has been a request to reorganize the workflow page as workflows have grown past basic and advanced.


http://bioconductor.org/help/workflows/


We wanted to check with the community what your thoughts were for categories.

Thank you for your suggestions.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Laurent Gatto
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On 15 December 2017 12:33, Shepherd, Lori wrote:

            

      
      
      
    

        
Could biocViews be used for this?

For example assign workflows biocViews of the packages they use (either
all biocViews or those that occur several times). biocViews aren't
perfect, put this would allow automation and would provide consistency
with the packages categorisation.

Best wishes,

Laurent

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Aaron Lun
    

    

      
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My proposed categories reflect my vested interests, but here goes:

- Gene expression:
    - rnaseqGene
    - RNAseq123
    - ExpressionNormalizationWorkflow
    - RnaSeqGeneEdgeRQL

- Epigenomics: (not quite sure what to call this)
    - chipseqDB
    - methylationArrayAnalysis
    - generegulation

- Single cell:
    - simpleSingleCell
    - cytofWorkflow (or in proteomics?)

- Proteomics:
    - proteomics
    - highthroughputassays
    - cytofWorkflow (see above)

- Variant calling:
    - Variant calling
    - Nucleotide tallies
    - eQTL

- Resource querying: (needs a better name)
    - recountWorkflow
    - TCGAWorkflow

- Other:
    - everything else.

I haven't looked at the Basic workflows, which are probably basic enough 
to be lumped together in that existing section.

-A

        
On 15/12/17 12:33, Shepherd, Lori wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Andrzej Oleś
    

    

      
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Hi,

Motivated by discussions with Aaron I've already started to group the
workflows on the page (but this change didn't propagate to the website
yet). Some common topics I was able to identify so far include:

- Beginner's Worklows authored originally by the core team giving a quite
broad overview of the BioC infrastructure
- Annotations
- RNA Sequencing
- Single-cell Workflows
- Genomic Variants
- Domain Specific

The domain-specific workflows currently includes the "advanced" ones which
focus on a particualar topic otherwise not covered by other workflows.

Cheers,
Andrzej

On Fri, Dec 15, 2017 at 1:33 PM, Shepherd, Lori <

        
Lori.Shepherd at roswellpark.org> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Andrzej Oleś
    

    

      
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Hi Laurent,

thanks, we might consider this in the future. To get us going, for the
moment we will probably just rearrange the website manually.

On the technical note: even though workflows are now fully fledged
packages, two documents linked from https://bioconductor.org/help/workflows
are just static PDFs. As they are around for some time now, I'm not sure
how up-to-date they are.

Cheers,
Andrzej

        
On Fri, Dec 15, 2017 at 1:56 PM, Laurent Gatto <lg390 at cam.ac.uk> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Andrzej Oleś
    

    

      
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Hi Aaron,

thank you for taking the lead. I've merged your suggested categories with
my preliminary arrangement (which just went online). I've also included an
index at the beginning of the page.

Any refinements are of course welcome, e.g. via PR to
https://github.com/Bioconductor/bioconductor.org

Cheers,
Andrzej

        
On Fri, Dec 15, 2017 at 2:08 PM, Aaron Lun <alun at wehi.edu.au> wrote:

        

            

      
      
      
    

        

      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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Thanks for this!


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Aaron Lun
    

    

      
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Thanks Andrzej. And yes, I just put in a PR; I hope itemized sublists 
for a particular workflow (i.e., mine) aren't too ambitious.

I'm thinking about whether "Epigenetics" is the right section heading. 
For greatest generality, you could call it "Genome regulation", which 
bundles all genomic binding/accessibility/methylation stuff together.

I was also pondering whether cytof belongs in Proteomics or Single-cell, 
given the equivalent FACS workflow lives in Proteomics and the nature of 
the data are fundamentally different from single cell genomics datasets. 
But I suppose that's none of my business, I'll leave it to Lukas & co.

It would be nice to see an image analysis workflow up there!

-A

        
On 15/12/17 15:27, Andrzej Ole? wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Michael Love
    

    

      
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This already looks much improved, thanks Andrzej and Aaron. I think
workflows are where it's at, and this page is probably
underappreciated by Bioconductor users and the outside community.

My wishlist for the workflows page, which may exceed what is available
for the current effort:

1) It should say at the top which version of R/Bioconductor the
workflows are being built on.

2) On the main page, for each workflow:

* A thumbnail (could live in a pre-specified location in the package)
* Author list (autopopulated from DESCRIPTION)
* Version
* Link to the (most current) F1000Research articles for those which
are published (new field in DESCRIPTION?)
* Some kind of CI "buttony" thing, to indicate to users that these are
live documents
* Key Bioc/R packages used in this worfklow (could this also be an
additional DESCRIPTION field?)

3) I think it would be good to encourage the more stubby workflow
descriptions to add more text, and maybe to decrease the very words
ones, so that it's more consistent. Wow, that's pretty obsessive of
me, but I think it would make the page look more professional.

4) Text somewhere with a link to the support site and how to ask for
help on workflows (e.g. vignette(), ?functionName)

5) An advertisement somewhere for submitting a workflow, link to more
detailed doc elsewhere

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Wolfgang Huber
    

    

      
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Thank you all for the efforts on this! I agree with Mike that there's a 
lot of yet untapped potential in the workflows, for all levels of BioC 
users: for beginners, to make their first steps, for more experienced 
users, to learn new stuff.

Mike's points 1-5 are great, I second them.

And then some polite pushback on categorization... I think for a volume 
of one-two dozen workflows, browsing based on short descriptions (Mike's 
point 3) will often be preferable. And if the volume gets larger, I 
noted that "search" rather than "manually curated hierarchical menu 
trees" drives many successful websites (Amazon, Google) and there's 
probably a lesson in there.

	Best wishes
		Wolfgang


15.12.17 16:55, Michael Love scripsit: