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OmicsBox supports COVID-19 projects

COVID-19 Research Project in Tunisia with OmicsBox Support

BioBam Supported Project – with OmicsBox. Researchers: Pr. Sami Aifa from the Laboratory of Molecular and Cellular Screening Processes (LPCMC) from the Centre of Biotechnology of Sfax, Tunisia Dr. Amor Mosbah from the Laboratory of Biotechnology and Valorization of Bio-Geo-Ressources (LBVBGR) from the Superior Institute of Biotechnology of Sidi Thabet, Tunisia  Dr. Salma Abdeljalil and Pr. Ali Gargouri from the

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OmicsBox supports COVID-19 projects

COVID-19 Research Project in Brazil with OmicsBox Support

BioBam Supported Project – with OmicsBox. Researchers: Luis Fernando Saraiva Macedo Timmers – Coordinator – Univates, Brazil Rafael Andrade Caceres – UFCSPA, Brazil Leandro de Mattos Pereira, UFRJ, Brazil Fernando Ruggiero Bachega – UFCSPA, Brazil Marcia Ines Goettert – Univates, Brazil Luiz Augusto Basso – PUCRS, Brazil Project: Currently, a large amount of data is available regarding the new SARS-CoV-2

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Solanum tuberosum

Identification and Expression analysis of genes involved in endodormancy break in potato (Solanum tuberosum L.)

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Madhuri Gupta Dr. Pushpender Kumar Project and Overview At harvest, potato (Solanum tuberosum L.) tubers, one of the most important crops among vegetables, are dormant and will not sprout. Tubers contain shoot apical meristems on their surface with the ability to differenciate and grow into a new clone of the parent plant.

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Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox

In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium

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Comparing taxonomic and functional compositions between metagenomic samples

Any annotation of metagenomic sequences, whether it involves pathways, clusters of orthologous genes, species or any other taxonomic or functional classification can be compared across samples. These analyses are encompassed within the Differential Abundance Analysis, and they require robust statistical approaches to achieve reliable results because metagenomics datasets often show under-sampling and low signal-to-noise ratios. All differential abundance analyses can

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Verminephrobacter eiseniae

Draft genome of a new Verminephrobacter eiseniae strain

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Mr. Arun Arumugaperumal Mr. Sayan Paul and Miss Saranya Lathakumari, PhD students Dr. Sudhakar Sivasubramaniam Abstract The earthworm Eisenia fetida has a symbiotic bacteria named Verminephrobacter eiseniae in its nephridia. A new strain of V. eiseniae msu was found out and the genome of the bacteria was found hidden in the genome

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Busco OmicsBox Screenshot

Exploring transcriptome completeness in OmicsBox with BUSCO

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. Once the assembly is complete, researchers need to know how good it is or compare the quality of similar assemblies generated by different parameters. There are several ways to characterize the quality of transcriptome assemblies. A good metric of assembly

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