21 papers · ranked by Valyu relevance
Haseeb A Khan
Biomedical scientists and clinicians often require customized and user-friendly software tools due to the unavailability of specific software, complexity of existing software or high cost of commercial software. This editorial provides a short update on recently published task-oriented biomedical software tools. The…
Haseeb Ahmad Khan
In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific…
Rex A. Cardan, Elizabeth L. Covington, Richard A. Popple
3.1### Software configuration When possible, editing of configuration parameters should be controlled to eliminate the risk of unintended changes. This is difficult to achieve at run-time because it requires the creation and management of user roles. If configuration parameters cannot be secured at run-time, developers…
Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon + 9 more
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both…
Abdulrazzaq Qasem Ali, Abu Bakar Md Sultan, Abdul Azim Abd Ghani, Hazura Zulzalil + 1 more
'Hazura Zulzalil' 'Stefan Wagner'] Despite the benefits of standardization, the customization of Software as a Service (SaaS) application is also essential because of the many unique requirements of customers. This study, therefore, focuses on the development of a valid and reliable software customization model for…
Gregor Ulm, Emil Gustavsson, Mats Jirstrand
OODIDA (On-board/Off-board Distributed Data Analytics) is a platform for distributing and executing concurrent data analytics tasks. It targets fleets of reference vehicles in the automotive industry and has a particular focus on rapid prototyping. Its underlying messagepassing infrastructure has been implemented in…
Masoud Jamei, Steve Marciniak, Duncan Edwards, Kris Wragg + 3 more
'Kairui Feng' 'Adrian Barnett' 'Amin Rostami-Hodjegan'] Developing a user-friendly platform that can handle a vast number of complex physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models both for conventional small molecules and larger biologic drugs is a substantial challenge. Over the last decade…
David A. Burdge, Igor G. L. Libourel, Vinod Scaria
Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can…
Georgi Danovski, Teodora Dyankova, Stoyno Stoynov
We present CellTool, a stand-alone open source software with a Graphical User Interface for image analysis, optimized for measurement of time-lapse microscopy images. It combines data management, image processing, mathematical modeling and graphical presentation of data in a single package. Multiple image filters…
Milot Mirdita, Martin Steinegger, Johannes Söding
The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST. The app is easy to install for…
Gunnar Kudrjavets, Jeff Thomas, Aditya Kumar, Nachiappan Nagappan + 1 more
'Ayushi Rastogi'] Abstract—Using custom memory allocators is an efficient performance optimization technique. However, dependency on a custom allocator can introduce several maintenance-related issues. We present lessons learned from the industry and provide critical guidance for using custom memory allocators and…
Oliver Rodríguez
Here, I introduce Soft Potato, an open source electrochemical simulator and toolkit that contains typical electrochemical equations and simulations to aid researchers streamline their data analysis when dealing with large datasets. As examples, I show here how to use it to calculate steady state voltammograms from…
K. V. Dmitriev, Shanza Ali Zafar, Kevin Schmiechen, Yi Lai + 6 more
'Micheal Saleab' 'Pranav Nagarajan' 'Daniel Dollinger' 'Markus Hochstrasser' 'Stephan Myschik' 'Florian Holzapfel'] Abstract—The emergence of a global market for urban air mobility and unmanned aerial systems has attracted many startups across the world. These organizations have little training or experience in the…
Inge M. N. Wortel, Johannes Textor
The Cellular Potts Model (CPM) is a powerful in silico method for simulating diverse biological processes at tissue scale. Because of its inherently graphical nature, this model should in theory be accessible to a large audience of biologists – without requiring extensive mathematical expertise. But in practice, CPMs…
Malcolm Sim, Mohammad Ghazi Vakili, Felix Strieth-Kalthoff, Han Hao + 4 more
Self-driving laboratories (SDLs), which combine automated experimental hardware with computational experiment planning, have emerged as powerful tools for accelerating materials discovery. The intrinsic complexity created by their multitude of components requires an effective orchestration platform to ensure the…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy + 3 more
Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, to allow users to easily…
Riccardo Smeriglio, Roberta Bardini, Alessandro Savino, Stefano Di Carlo
In computational biology, in silico simulators are vital for exploring and understanding the behavior of complex biological systems. Hybrid multi-level simulators, such as PhysiCell and PhysiBoSS 2.0, integrate multiple layers of biological complexity, providing deeper insights into emergent patterns. However, one key…
Djamal Ziani
Software as a Service (SaaS) becomes in this decade the focus of many enterprises and research. SaaS provides software application as Web based delivery to server many customers. This sharing of infrastructure and application provided by Saas has a great benefit to customers, since it reduces costs, minimizes risks…
Jay Jay Billings, Andrew Bennett, Jordan H. Deyton, Kasper Gammeltoft + 9 more
'Kasper Gammeltoft' 'Jonah Graham' 'Dasha Gorin' 'Hari B. Krishnan' 'Menghan Li' 'Alexander McCaskey' 'Taylor Patterson' 'Robert Smith' 'Gregory R. Watson' 'Anna Wójtowicz'] Jay Jay Billings 1 , 2 , Andrew R. Bennett 1 , 3 , Jordan Deyton 1 , 4 , Kasper Gammeltoft 1 , 5 , Jonah Graham 6 , Dasha Gorin 1 , 7 , Hari…
Nadir K. Salih, Tianyi Zang
Cloud computing is a new technology widely studied in recent years. Now there are many cloud platforms both in industry and in academic circle. How to understand and use these platforms is a big issue. A detailed comparison has been presented in this paper focused on the aspects such as the architecture…