A forum for conversations about published paper

Q:
I saw your paper "Structuring supplemental materials in support of reproducibility" and appreciate your points. I would love to see a forum (like GATK’s forum or StackOverflow) where each topic for a conversation thread is a single published paper. Then everyone who is trying to replicate results could post their questions and authors their answers for all to see. I think this would be much better than the current closed system of emailing the authors. I would love to see a day when a link to a forum is provided on papers, rather than the authors’ email addresses.Who would have the ability to make something like this get started and catch on? Do you know if they are thinking about funding a platform for something like this at the NIH?

A:
with respect to "Who would have the ability to make something like this get started and catch on?"
maybe plos

with respect to "Do you know if they are thinking about funding a platform for something like this at the NIH?"
don’t know

Permission to use images

Q:
I have been using the Genboree exceRpt workflow, and loving it! It has saved me so much time! Your paper got me on to it, and I would like to use one of the figures (1) of the exceRpt pipeline in my PhD thesis. Am I right to contact you to request permission? Or should I be heading to Cell for this?

A:
fine w/ me – just acknowledge us (see
https://sites.gersteinlab.org/permissions/)

source code for context-specific TF co-association analysis in ‘Architecture of the human regulatory network derived from ENCODE data’

Q:
I have benefited a lot from you work entitled ‘Architecture of the human regulatory network derived from ENCODE data’ and I want to use the framework you developed for context-specific TF co-association analysis. However, I can’t find the source code at your given address http://code.google.com/p/tf-co-association/. Do you have the replaced address to share the source code for that?

A:
Is this what you are looking for?
https://code.google.com/archive/p/tf-coassociation/source/default/source

Regulatory Genetic network AND DSPN

Q:
I am studying your publication in Science (Comprehensive functional genomic resource and integrative model for the human brain, Science 362,1266(2018) with great interest. As a quantitative geneticist, I found it very relevant to the study of complex genetic traits. Therefore, I am writing this note to request your assistance inorder get your software/algorithm for Regulatory Genetic Network modeling and Integrative deep learning model (DSPN) so that we could implement them at NIH supercomputer system and conduct some integrative genomic modeling work in the area of brain/neuropsychiatry.

A:
Best to see resource.psychencode.org. Specifically — you can find the matlab codes "7. Matlab code and formatted data for
the DSPN" on http://resource.psychencode.org/