Description

The Bioinformatics platform develops algorithms to unravel omics data, from wet-lab to publication-ready results. Our scripts for data analysis are realized with open-source language, i.e., R and Phyton. When interested in specific pathologies or experimental conditions, we often take advantage of the large existing data repositories, such as GEO and Arrayexpress, where huge high throughput datasets are published. On the other hand, we also assist researchers in the design of experimental protocols and the analysis of the generated datasets, with custom curated methods.

In addition, we are also able to generate novel transcriptomic/genomic data, by using the new sequencing technology developed by Oxford Nanopore. To this end, the platform is equipped with a Cellular and Molecular Biology lab, used also to validate computationally predicted biological interactions.

Expertise

• Descriptive statistics and inferential statistics.
• High throughput data analysis, i.e. Next Generation Sequencing or microarray based technologies.
• Machine Learning based predictive algorithms.
• Big Data management and analysis
• Network analysis
• Transcriptomics/genomics data generation

Facilities & Equipment

Software

The scripts used to perform custom data analysis are written in open-source languages, e.g. R and Bioconductor libraries or Python. Interaction networks can be visualized with Pajek and Cytoscape. The proprietary software Ingenuity Pathway Analysis is used to perform consolidated bioinformatics data analysis pipelines. 

Hardware

• 3 workstation
• Server – CPU: 2x Xeon Gold 6152 2.10 GHz 22 Cores RAM: 128GB
• Server – CPU: 2x AMD Epyc 7402 24 Cores 2.8GHz RAM: 256GB HDD: 3x 480GB SSD GPU: 2x Nvidia A100 40GB

Wet lab

• Cellular and Molecular Biology lab
• multimodal plate reader BioTek Synergy H1
• Oxford Nanopore MinION Mk1c