MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, .

The genome of () DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.

BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.

The process of navigating through the landscape of biomedical literature and performing searches or combining them with bioinformatics analyses can be daunting, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related repositories. Herein, we present BioTextQuest v2.0, a tool for biomedical literature mining.

Biology's transformation: from observation through experiment to computation.

Summary: We explore the nuanced temporal and epistemological distinctions among natural sciences, particularly the contrasting treatment of time and the interplay between theory and experimentation. Physics, an exemplar of mature science, relies on theoretical models for predictability and simulations. In contrast, biology, traditionally experimental, is witnessing a computational surge, with data analytics and simulations reshaping its research paradigms.

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA.

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role.

A choice, not an obligation : Releasing scientific software as open source should be the responsibility of the authors.

The timing of making software open source should not be dictated by journal guidelines. [Image: see text]