FAANG List Archived Post

From apache@animalgenome.org  Mon Aug 28 15:33:23 2017
From: "Kasimanickam, Vanmathy" <vkasiman@vetmed.wsu.edu>
Subject: RE: FAANG Integrative Genomics and Network Biology analysis
Date: Mon, 28 Aug 2017 18:45:12 +0000
To: FAANG Members <faang@animalgenome.org>

Hello Rob,

Will the subgroup be developing something similar to the software "ingenuit=
y pathway analysis" to integrate biological functions and others, but with =
the specific focus on various animals species (from lab animal to large ani=
mal 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 robust=
ly
   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 inference=
s
   from integrated  data and to develop recommended methods for establishin=
g
   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 issue=
s
   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 genom=
ics
   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.eduMolly McCue, University of Minnesota,
mccu0173umn.eduCarolina Correia,
University College Dublin, carolina.correiaucdconnect.ieThomas Hall, University College
Dublin, thomas.hallucdconnect.ieDavid MacHugh, University College
Dublin, david.machughucd.ie
--
____________________________
Rob Schaefer, PhD

USDA-NIFA Postdoctoral Fellow
Equine Genetics and Genomics Lab
University of Minnesota
@CSciBio