Automated relative binding free energy calculations: from SMILES to ΔΔG
In drug discovery, computational methods are a key part of making informed design decisions and prioritising compounds. In particular, optimizing compound affinity is
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workflow
PyCOMPSs as an instrument for Translational Computer Science
This paper describes our experience with the PyCOMPSs project, a programming model for distributed computing. While it is a research instrument for our team, it has also been applied in multiple real use cases under the umbrella of European Funded projects or as part of internal projects between various departments at the Barcelona Supercomputing Center (BSC). The paper illustrates how the authors have engaged in TCS as an underlying research methodology, collecting experiences from three European projects.
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Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
Here we present the Common Workflow Language (CWL) project, which produces free and open standards for describing command-line tool based workflows. The CWL standards provide a common but reduced set of abstractions that are both used in practice and implemented in many popular workflow systems.
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BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) of fering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library.
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Ten Simple Rules for making a software tool workflow-ready
There is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow.
In this paper we present 10 simple rules for how a software tool can be prepared for workflow use
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Making Canonical Workflow Building Blocks interoperable across workflow languages
We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.
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