PREGO hackathon

PREGO team and collaborators, we all met at 28 March - 1 April 2019, Lato Hotel, Heraklion Center by the venetian port to brainstorm, desing and implement the initial steps of PREGO. Aims of this kick off meeting was to pave the ground for the PREGO project both in technical (software development) and scientific terms (publication, show cases). PREGO is a three-year long Hellenic Foundation for Research and Innovation project. It builds on previously developed text mining and data integration components. The latter are customized to collect metagenomics, metagenetics, and barcoding pertinent input (literature and record text fields that is) for subsequence mining of microorganism, environment type and process (biological, geochemical, anthropogenic) association.

Participants

Dr. Evangelos (Vangelis) Pafilis (IMBBC, HCMR, data integration and literature mining, HPC coordination) Dr. Lars Juhl Jensen (Uni of Copenhagen, NNF CPR, protein networks, Proteomics support, STRING, text mining and data integration) Dr. Georgios Pavlopoulos (BSRC Alexander Fleming, Athens, data integration, network analysis and visualization, metagenomics, immunology collaborators) Dr. Christina Pavloudi (IMBBC, HCMR, Microbial ecology, literature curator, marine sediment and water column, statistics (in R), NGS lab (MiSEQ, MinION) Mr. Haralampos (Haris) Zafeiropoulos (IMBBC, HCMR, microbial ecology, ecological networks and community dynamics, bioinformatics, HPC, PREGO PhD student) Ms. Ioulia Santi (IO & IMBBC, HCMR, IO: Inst. of Oceanography, plankton ecology Mr. Georgios Tsamis (IMBBC, HCMR, Web devel, embedded systems (ARM)) Dr. Anastasia Tsiola (IO, HCMR, atsiola@hcmr.gr, marine plankton and virome (informed)

Actions

Hardware setup A dedicated server (Dell PowerEdge R540, 20cores/40threads Intel Silver, 64GB RAM, 2.4TB (usable, RAID1, 12Gbps data transfer) arrived at IMBBC on the 20th February 2019. We installed software and performed data gathering preparations

Software Prototype / Data Analysis Summarization, Overall Discussion and Feedback

Defined use cases (ie. scientific knowledge questions to address) like: “I would like to find out more about microbes significantly associated with heavily polluted ports” “I would like to find out more about microbes significantly associated with sampling site linked to sulfur-cycling” “I would like to find out more about microbes significantly associated with cultured types of soils (avail as an EnvO list of terms) that have been treated with specific fertilizer (e.g. N or P or NP enriched)” “Where has a species been found, ocean, arctic?” “Has a microbe been seen in other hosts, e.g. has a sponge related bacterium been found e.g. in coral reefs?” (organism - organism interaction) “Are there different genes related to a specific process in different environments”

What a great meeting to start a project!

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