Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.

In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival.

Global challenges and microbial biofilms: Identification of priority questions in biofilm research, innovation and policy.

Priority question exercises are increasingly used to frame and set future research, innovation and development agendas. They can provide an important bridge between the discoveries, data and outputs generated by researchers, and the information required by policy makers and funders. Microbial biofilms present huge scientific, societal and economic opportunities and challenges.

Convergence research and training in computational bioengineering: a case study on AI/ML driven biofilm-material interaction discovery.

Initially, research disciplines operated independently, but the emergence of trans-disciplinary sciences led to convergence research, impacting graduate programs and research laboratories, especially in bioengineering and material engineering as presented here. Current graduate curriculum fails to efficiently prepare students for multidisciplinary and convergence research, thus creating a gap between the students and research laboratory expectations. We present a convergence training framework for graduate students, incorporating problem-based learning under the guidance of senior scientists and collaboration with postdoctoral researchers.

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.

The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study used G20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text.

BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of Biomedical and Biofilm Image Datasets.

Micrograph comparison remains useful in bioscience. This technology provides researchers with a quick snapshot of experimental conditions. But sometimes a two- condition comparison relies on researchers' eyes to draw conclusions.

Bio-TDS: bioscience query tool discovery system.

Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB.

The BioExtract Server: a web-based bioinformatic workflow platform.

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user.

Computational analysis of a novel SACS gene mutation with BioExtract server.

Autosomal recessive spastic ataxia of Charlevoix-Saguenay is a distinct form of hereditary early-onset spastic ataxia caused by cerebellum and spinal cord degeneration. The SACS gene has been demonstrated to be responsible for the disease through worldwide description of different mutations. We report here a computational analysis of a novel SACS gene mutation identified in a Tunisian family, using workflow implemented on the BioExtract Server.

BioExtract server--an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data.

Many in silico investigations in bioinformatics require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community databases, and project databases for use in domain-specific research. Different data sources frequently utilize distinct query languages and return results in unique formats, and therefore researchers must either rely upon a small number of primary data sources or become familiar with multiple query languages and formats.

Implementing bioinformatic workflows within the bioextract server.

Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.

PlantGDB: a resource for comparative plant genomics.

PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae).

Comparative plant genomics resources at PlantGDB.

PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences.