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 manuscript. One has a few useful scripts attached, I will make them available with the data as soon as it 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 A newer version of the script, which comes handy when using FMBN 2.0 edge tables and allows to generate files which can be used with the package Bipartite of R (more on this later)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.

Carpe diem

The article describing FoodMicrobionet

Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2015. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. International Journal of Food Microbiology, 219, 28-37

can be downloaded at:

http://authors.elsevier.com/a/1SDa5cF3hnw6p

The link will expire on February 5, 2016. Enjoy

Version 1.0.3 has just been published

After a long and difficult reviewing process the first paper on FoodMicrobionet has just been published: Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2015. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. International Journal of Food Microbiology, 219, 28-37 doi:10.1016/j.ijfoodmicro.2015.12.001. Click here to access the paper on ScienceDirect.

We would very much appreciate your opinion on this.