ARTICLE | doi:10.20944/preprints202003.0043.v1
Subject: Earth Sciences, Environmental Sciences Keywords: Groundwater Modeling; Hydrologic Monitoring Network; American Samoa; Jupyter Notebooks; GitHub; Python
Online: 3 March 2020 (11:45:15 CET)
Recent advancements in cloud-computing and social-networking are influencing how we communicate professionally, work collaboratively, and approach data-science tasks. Here we show how the groundwater modeling field is well positioned to benefit from these advancements. We present a case study detailing a vertically-integrated, collaborative modeling framework jointly developed by participants at the American Samoa Power Authority and at the University of Hawaii Water Resources Research Center. The framework components include direct collection and analysis of climatic and streamflow data, development of a water budget model, and initiation of a dynamic groundwater modeling process. The framework is entirely open-source and applies newly available data-science infrastructure using Python-based tools compiled with Jupyter Notebooks and cloud computing services such as GitHub. These resources allow for seamless integration of multiple computational components into a dynamic cloud-based workflow that is immediately accessible to stakeholders, resource managers, or anyone with an internet connection
Subject: Life Sciences, Biochemistry Keywords: enzyme kinetics; Jupyter notebook; kinetic modelling; matplotlib; NMR spectroscopy; optimisation; parametrisation; PySCeS; SciPy; validation
Online: 11 June 2019 (11:15:01 CEST)
Bottom-up systems biology entails the construction of kinetic models of cellular pathways by collecting kinetic information on the pathway components (e.g. enzymes) and collating this into a kinetic model, based for example on ordinary differential equations. This requires integration and data transfer between a variety of tools, ranging from data acquisition in kinetics experiments, to fitting and parameter estimation, to model construction, evaluation and validation. Here, we present a workflow that uses the Python programming language, specifically the modules from the SciPy stack, to facilitate this task. Starting from raw kinetics data, acquired either from spectrophotometric assays with microtitre plates or from NMR spectroscopy time courses, we demonstrate the fitting and construction of a kinetic model using scientific Python tools. The analysis takes place in a Jupyter notebook, which keeps all information related to a particular experiment together in one place and thus serves as an e-labbook, enhancing reproducibility and traceability. The Python programming language serves as an ideal foundation for this framework because it is powerful yet relatively easy to learn for the non-programmer, has a large library of scientific routines and active user community, is open-source and extensible, and many computational systems biology software tools are written in Python or have a Python API. Our workflow thus enables investigators to focus on the scientific problem at hand rather than worrying about data integration between disparate platforms.
ARTICLE | doi:10.20944/preprints202112.0356.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: quantum computing; quantum computing framework; quantum simulator; quantum technology; quantum theory; quantum mechanics; quantum circuit; quantum algorithm; ibm qiskit; notebooks jupyter
Online: 22 December 2021 (12:00:48 CET)
The shortage of quantum computers, and their current state of development, constraints research in many fields that could benefit from quantum computing. Although the work of a quantum computer can be simulated with classical computing, personal computers take so long to run quantum experiments that they are not very useful for the progress of research. This manuscript presents an open quantum computing simulation platform that enables quantum computing researchers to have access to high performance simulations. This platform, called QUTE, relies on a supercomputer powerful enough to simulate general purpose quantum circuits of up to 38 qubits, and even more under particular simulations. This manuscript describes in-depth the characteristics of the QUTE platform and the results achieved in certain classical experiments in this field, which would give readers an accurate idea of the system capabilities.