24 papers · ranked by Valyu relevance
Zachary Caterer, Rachel V. Horejsi, Carly Weber, Blake Mathisen + 9 more
Image-based phenotypic screening is a fundamental technique used to better understand the basic biology of helminths and advance discovery of new anthelmintics. Miniaturization of screening platforms and automated microscopy have led to a surge in imaging data and necessitated software to organize and analyze these…
Ye, Jiabo, Zhang, Xi + 26 more
This paper introduces GUI-Owl, a foundational GUI agent model that achieves new stateof-the-art performance among open-source end-to-end models across ten GUI benchmarks spanning both desktop and mobile environments, covering grounding, question answering, planning, decision-making, and general procedural knowledge in…
Jie Mu, Chaoyun Zhang, Chiming Ni, Lu Wang + 14 more
We introduce GUI-360◦ , a large-scale, comprehensive dataset and benchmark suite designed to advance computer-using agents (CUAs). CUAs present unique challenges and is constrained by three persistent gaps: a scarcity of real-world CUA tasks, the lack of automated collection-and-annotation pipelines for multimodal…
ZACHARY CATERER, RACHEL V. HOREJSI, CARLY WEBER, BLAKE MATHISEN + 9 more
'CHASE NELSON' 'MAGGIE BAGATTA' 'IRELAND COUGHLIN' 'MEGAN WETTSTEIN' 'ANKIT KULSHRESTHA' 'HUI SIANG BENJAMIN LEE' 'LEONARDO R. NUNN' 'MOSTAFA ZAMANIAN' 'NICOLAS J. WHEELER'] Image-based phenotypic screening is a fundamental technique used to better understand the basic biology of helminths and advance discovery of new…
Zachary Caterer, Rachel V. Horejsi, Carly Weber, Blake Mathisen + 9 more
'Chase N. Nelson' 'Maggie Bagatta' 'Ireland Coughlin' 'Megan Wettstein' 'Ankit Kulshrestha' 'Hui Siang Benjamin Lee' 'Leonardo R. Nunn' 'Mostafa Zamanian' 'Nicolas J. Wheeler'] Image-based phenotypic screening is a fundamental technique used to better understand the basic biology of helminths and advance discovery of…
Chaoyun Zhang, Shilin He, Jiaxu Qian, Bowen Li + 9 more
—Graphical User Interfaces (GUIs) have long been central to human-computer interaction, providing an intuitive and visually-driven way to access and interact with digital systems. Traditionally, automating GUI interactions relied on script-based or rule-based approaches, which, while effective for fixed workflows…
Rashid Hussain, Andrew Scott Hackett, Sandra Álvarez-Carretero, Lydia Tabernero + 1 more
Virtual screening of large chemical libraries is essential to support computer-aided drug development, providing a rapid and low-cost approach for further experimental validation. However, existing computational packages are often for specialised users or platform limited. Previously, we developed VSpipe, an…
Authors not listed
nDTomo is a Python-based software suite for the simulation, reconstruction and analysis of X-ray chemical imaging and computed tomography data. It provides a collection of Python function-based tools designed for accessibility and education as well as a graphical user interface (GUI). Prioritising transparency and ease…
Hyeon-Min Kim, Hwayeon Jeong, Abyot Melkamu Mekonnen, Yeongjun Kim + 4 more
Large language models (LLMs) are increasingly used to generate bioinformatics pipelines and to carry out analyses from natural-language prompts. However, the resulting analyses are often difficult to reproduce across sessions, owing to the non-deterministic nature of LLM-driven conversations and heterogeneity of local…
Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen
This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories: https://github.com/martin-sicho/genui https://github.com/martin-sicho/genui-gui…
Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot + 1 more
'Roeland CHJ van Ham'] Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses…
Authors not listed
We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step 2) the formal (platform independent) specification of the GUI, and (Step 3) the…
Yibin Xu, Liang Yang, Hao Chen, Hua Wang + 2 more
The limitation of graphical user interface (GUI) data has been a significant barrier to the development of GUI agents today, especially for the desktop / computer use scenarios. To address this, we propose an automated GUI data generation pipeline, AutoCaptioner, which generates data with rich descriptions while…
Eric Deutsch, Luis Mendoza, David Shteynberg, Michael Hoopmann + 3 more
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search…
Hesam Dashti, Jonathan R. Wedell, Gabriel Cornilescu, Charles D. Schwieters + 3 more
Computational molecular dynamics, energy minimization, and modeling of molecular interactions are widely used in studies involving natural products, metabolites, and drugs. Manually directed computational steps commonly utilize an evolving collection of experimental and computational data, to which new data sources are…
Bruno Dantas, Calmenelias Fleitas, Alexandre P. Francisco, José Simão + 1 more
'José Simão' 'Cátia Vaz'] Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the following is true for many areas of science: published…
Markus Joppich, Ralf Zimmer, Joseph Gillespie
Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface…
Authors not listed
Solubility is the maximum amount of solutes that can dissolve in a certain amount of solvent at a certain temperature, and it is significant in battery electrolyte research since it confines the design space. Thus, solubility measurement is a critical constraint on running self-driving labs for battery electrolyte…
Authors not listed
Exploring electronic states in actinide compounds is a critical aspect of nuclear science. However, considering relativistic effects and electron correlation in theoretical calculations poses a complex challenge. To tackle this, we developed the CASPT2/RASPT2 program along with the DIRAC program, enabling calculations…
Yann Spöri, Jean-François Flot
Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Jochen Sieg, Christian Wolfgang Feldmann, Jennifer Hemmerich, Conrad Stork + 3 more
The open-source package scikit-learn provides various machine learning algorithms and data processing tools, including the Pipeline class, which allows users to prepend custom data transformation steps to the machine learning model. We introduce the MolPipeline package, which extends this concept to chemoinformatics by…
Daniel M. Jenkins, Ryan Kurasaki
Advances in scientific knowledge are increasingly supported by a growing community of developers freely sharing new hardware and software tools. In this spirit we have developed a free Android app, ABE-VIEW, that provides a flexible graphical user interface (GUI) populated entirely from a remote instrument by…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed…