New version posted

I have included material on a new version of FMBN (2.0.3) in the versions page. I will start now collecting material for a new version. If you are interested to contribute contact me. You can download instructions and templates for submission here.

Why should you contribute?

Contributors receive new versions of FoodMicrobionet and R scripts as soon as they are ready and are entitled to assistance in the use of the software for data extraction and analysis. In general, I am more inclined to use data received from authors of published papers (and include the data in FoodMicrobionet in a way that matches what has been published). However, we are also including material obtained by directly processing projects deposited in SRA and ENA with a standardised pipeline. The whole issue about FMBN is to make data (which in most cases are already deposited in public repositories) freely available in an easy(ish) to use format. So, why bother contributing if you can get data and scripts anyway? Well, as a contributor you get the data and scripts 6-9 months before they are made public and you can freely use them for your metastudies and reviews. The only thing we require is that you cite the source and the relevant published papers.

Long time, no see

A few updates. We are apparently on omics.com https://omictools.com/foodmicrobionet-tool

Feel free to review our web site.

Plus, with Danilo Ercolini, Francesca De Filippis and Teresa Zotta we have submitted a couple of manuscripts. One has a few useful scripts attached, I will make them available with the data as soon as the manuscript is accepted (however, if you are shrewd enough you can find them yourself). The other is on microbial association networks (guest star Karoline Faust, whom I thank).

FMBN@FM2016

Two posters related to FoodMicrobionet will be on display at FoodMicro 2016, Dublin. I am afraid that the quality of the images on the posters is not the best (but they fold nicely in a suitcase). You can see the images at higher resolution in the .pdf versions.

  • PO2-FS-080 – FOODMICROBIONET 1.1.6: A NETWORK ANALYSIS TOOL FOR THE EXPLORATION OF FOOD BACTERIAL COMMUNITIES. Eugenio Parente*, Francesca De Filippis , Teresa Zotta, Paul Cotter , Orla O’Sullivan, Edoardo Puglisi, Danilo Ercolini.
  • PO2-FS-109 – A COMPARISON OF BIOINFORMATICS PIPELINES FOR THE ANALYSIS OF 16S METAGENOMICS DATA OF FOOD MICROBIAL COMMUNITIES, Francesca De Filippis, Danilo Ercolini, Eugenio Parente.

See you in Dublin!

Transforming an edge table into an abundance table

I have just published a new script to transform an edge table in an OTU abundance table. Using this you can (if you so wish) transform the whole FoodMicrobionet dataset (or part of it) in a very large abundance table. A newer version of the script, which comes handy when using FMBN 2.0 edge tables and allows to generate files which can be used with the package Bipartite of R (more on this later) is available here. Be careful with this script, however, it must be run in pieces.