FAANG List Archived Post

From apache@animalgenome.org  Mon Aug 28 15:34:10 2017
From: Robert Schaefer <schae234@umn.edu>
Date: Mon, 28 Aug 2017 19:33:13 +0000
Subject: Re: FAANG Integrative Genomics and Network Biology analysis
       sub-group
To: FAANG Members <faang@animalgenome.org>

Hello Vanmathy,

Thanks for the question.

The group wont try to replace or specifically implement tools such as IPA,
rather it will focus on forming guidelines around how to approach network
analysis given the data being generated by FAANG. This is likely to include
recommendations using existing tools, i.e. if a group is successful doing
analysis using IPA (or some other tool) in one FAANG species, how do we
generalize it to be used in another species. Likewise, if a network or
integrative approach fails to work, we would like to catalog why this is so
(is it because its in an agricultural vs laboratory animal).

As we are just forming, we are first looking for research groups who are
asking integrative and network based questions so we can form a community
that is supportive and collaborative.

Thanks,
Rob

On Mon, Aug 28, 2017 at 1:45 PM Kasimanickam, Vanmathy <
vkasimanvetmed.wsu.edu> wrote:
> Hello Rob,
>
> Will the subgroup be developing something similar to the software
> "ingenuity pathway analysis" to integrate biological functions and others,
> but with the specific focus on various animals species (from lab animal to
> large animal species)?
>
>
> Vanmathy
>
> Vanmathy Kasimanickam DVM, MS, DACVPM
>
> ________________________________________
> From: Robert Schaefer [schae234umn.edu]> Sent: Monday, August 28, 2017 8:13 AM
> To: FAANG Members
> Subject: FAANG Integrative Genomics and Network Biology analysis sub-group
>
> Dear FAANG community members and friends,
>
> After seeing many posters and talks on data generation, collection, and
> curation from the animal genetics community at the recent ISAG meeting it
> has become clear that much progress has been made to achieve the aims set
> out by FAANG. Many of the relevant data sets (e.g. RNA-Seq, Chip-Seq,
> DNase-Seq etc) are currently being generated and some data sets are already
> available.
>
> As such, we have seen groups starting to analyze these data and developing
> pipelines that integrate and compare data across different data types,
> especially in the form of biological networks. To comply with the goals of
> FAANG, we are proposing to form a sub-group within the current
> Bioinformatics and Data Analysis working group that will focus on
> Integrative Genomics and Network Biology.
>
> This new sub-group would complement the current Bioinformatics and Data
> Analysis group and would have several specific goals:
>
>
>    - Generate a panel of recommended methods and software tools that
> robustly
>
>
>    integrate different data types with a focus on network analysis and to
>    provide feedback on the quality of and feasibility of integrated/network
>    approaches.
>
>    - Define community standards for statistical methods that make
> inferences
>
>
>    from integrated  data and to develop recommended methods for
> establishing
>    statistical significance (e.g. making sense of correlations and
> profiles).
>
>    - The group would discuss and evaluate database and storage methods for
>
>
>    large biological networks using FAANG data.
>
>    - The group would advise other FAANG groups on experimental design
> issues
>
>
>    relevant to downstream integrative genomics and network biology analyses
>    (e.g. minimum sample sizes required for correlation-based network
>    approaches).
>
>    - The group would establish an active, inclusive and friendly community
>
>
>    for animal scientists interested in the application of integrative
> genomics
>    and network biology.
>
>
>
> To start, current FAANG members can simply join the Integrative Genomics
> and Network Biology mailing list (faang-analysis-networkanimalgenome.org)> at http://www.faang.org/. 
Anyone who is not currently a member of FAANG
> is
> welcome to join the community via the above website.
>
>
> Additionally, we have started a GitHub page that will be used to to
> contribute code or discuss computational pipelines. Visit
> https://github.com/FAANG/faang-network-biology to get started. Information
> on how to contribute as well as community guidelines are specified in the
> repository.
>
>
> Sincerely,
>
> Rob Schaefer, University of Minnesota, schae234umn.edu> Molly McCue, University of Minnesota,
mccu0173umn.edu> Carolina Correia,
University College Dublin,
> carolina.correiaucdconnect.ie>
Thomas Hall, University College Dublin, thomas.hallucdconnect.ie> David MacHugh, University College
Dublin, david.machughucd.ie>
> --
> ____________________________
> Rob Schaefer, PhD
>
> USDA-NIFA Postdoctoral Fellow
> Equine Genetics and Genomics Lab
> University of Minnesota
>
> @CSciBio