Investigations

The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...

The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model ...

An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.

Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. Participating in BioCreative Track NLM-Chem we focus identifying chemicals in full-text articles (i.e. named entity recognition and normalization).

Virtual Tissues (VTs) are multi-scale, multi-cellular, mechanistic Agent Based Models (ABMs) that predict the spatio-temporal dynamics of biological tissues. While multiple platforms exist for constructing and executing VT models (listed below in the section on VT Modeling Frameworks), models developed for different platforms are currently incompatible and not accessible or executable in a common location, impeding model discovery, validation and reuse. FAIRSPACE will initially provide support ...

Consortium website: https://covidclinical.net/

Slack: https://c19i2b2.slack.com/ Owner: Nils Gehlenborg (nils@hms.harvard.edu)

i2b2 tranSMART Foundation Call to Action: https://transmartfoundation.org/covid-19-call-to-action/

Governments and policymakers take different measures vis-à-vis the COVID-19 crisis, ranging from advice to reduce social activities, to a complete lock down of society and economy. To support them with tools that enable them to fulfill their tasks we constructed a differential equation model for the COVID-19 epidemics using systems biology methodologies.

Data integration is an essential part of Systems Biology. Scientists need to combine different sources of information in order to model biological systems, and relate those models to available experimental data for validation. Currently, only a small fraction of the data and models produced during Systems Biology investigations are deposited for reuse by the community, and only a smaller fraction of that data is standards compliant, semantic content. By embedding semantic technologies into familiar ...