Generation and maintenance of Bioinformatics data repositories, data analysis tools, and web platforms

Bioinformatics databases, especially web databases, as well as bioinformatics visualization software, are crucial tools for biomedical research. In our group, we have developed graph databases, galaxy instances, R-shiny packages, and jupyter notebooks, among other bioinformatics tools. Our goal has been to create tools that are interactive, friendly, reproducible, and extensible, for both scientific and educational purposes.

Some of our tools include: (i) GREG (Gene Regulation Graph Database), which is an integrative graph database combining chromatin-chromatin, protein-chromatin, protein-protein, and lncRNA-chromatin data, into a single network, and allowing the user to explore genomic regions, specific genes, directly manipulate the network or perform network analyses from our website [1]. (ii) GSA-Central (Gene Set Analysis Central), which is a website with multiple tools (R-shiny packages, jupyter notebooks, and galaxy instances) for learning gene set analysis / pathway analysis, getting a comprehensive state-of-the-art of the existing tools, and accessing some tools through a Galaxy interface, among others [2,3]. We have also used GSA-Central to perform an analysis of the popularity versus the performance of bioinformatics software [2]. (iii) DynBioNet (Dynamic Biological Network Explorer): We have created a tool to manage and analyze dynamic networks, which we are using for both chromatin interaction and cell-cell interaction network analyses [4]. Our current plans include: (iv) A web platform for known and predicted cell-cell interaction networks.

References:

[1] MEI S, HUANG X, XIE C, and MORA A (2020), GREG—studying transcriptional regulation using integrative graph databases, Database, 2020, baz162 [Website]
[2] XIE C, JAUHARI S, and MORA A (2021), Popularity and performance of bioinformatics software: the case of gene set analysis, BMC Bioinformatics, 22;191 [Website]
[3] HUANG X, LU X, XIE C, JAUHARI S, XIE Z, MEI S, and MORA A (2022), GSA Central—A web platform to perform, learn, and discuss gene set analysis, Frontiers in Medicine, 9 [Website]
[4] Ongoing work [Website]