A5051114531- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Protein Structure and Dynamics
- Biomedical and Engineering Education
- Microbial Metabolic Engineering and Bioproduction
- Business Process Modeling and Analysis
- Advanced Data Storage Technologies
- Viral Infectious Diseases and Gene Expression in Insects
- Research Data Management Practices
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Genetics, Bioinformatics, and Biomedical Research
- Lung Cancer Treatments and Mutations
- Computational Drug Discovery Methods
- DNA and Nucleic Acid Chemistry
- Mass Spectrometry Techniques and Applications
- Enzyme Structure and Function
- Bacteriophages and microbial interactions
- Spectroscopy and Quantum Chemical Studies
- RNA and protein synthesis mechanisms
- 3D Printing in Biomedical Research
- Genomics and Phylogenetic Studies
- Cell Image Analysis Techniques
- Advancements in Semiconductor Devices and Circuit Design
- Algorithms and Data Compression
Universitat Politècnica de Catalunya
2012-2024
Barcelona Supercomputing Center
2012-2024
Institute for Research in Biomedicine
2014-2015
Universitat de Barcelona
2012-2014
Abstract Summary: MDWeb and MDMoby constitute a web-based platform to help access molecular dynamics (MD) in the standard high-throughput regime. The provides tools prepare systems from PDB structures mimicking procedures followed by human experts. It inputs can send simulations for three of most popular MD packages (Amber, NAMD Gromacs). Tools analysis trajectories, either provided user or retrieved our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. has two ways access,...
Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates largest amounts of data, and is using amount CPU time in supercomputing centres. MD trajectories are obtained after months calculations, analysed situ, practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists nucleic acids world. We present here a novel database system store analyses acids. The initial data set...
Abstract In the recent years, improvement of software and hardware performance has made biomolecular simulations a mature tool for study biological processes. Simulation length size complexity analyzed systems make both complementary compatible with other bioinformatics disciplines. However, characteristics packages used simulation have prevented adoption technologies accepted in fields like automated deployment systems, workflow orchestration, or use containers. We present here...
The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse process, reasonable timescales, the large generated amounts molecular data. In light this, we have developed present here pyPcazip: a suite for compression analysis dynamics (MD) compatible with trajectory file formats by most contemporary MD engines such as AMBER, CHARMM, GROMACS NAMD, MPI parallelised to permit efficient processing very datasets. pyPcazip Unix based open-source...
Abstract We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to collection of transversal pre-configured biomolecular simulation workflows assembled with the library. Available include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in platform or downloaded run users’ own premises. Remote launching long executions user's available High-Performance...
The SEABED web server integrates a variety of docking and QSAR techniques in user-friendly environment. goes beyond the basic tools implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. is not monolithic workflow tool but Software as Service platform.SEABED free available at http://www.bsc.es/SEABED.
Abstract We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology describing and wrapping computational tools, in order for them to be utilised reproducible manner from multiple workflow languages execution platforms. The is implemented demonstrated with BioExcel library (BioBB), collection tool wrappers field biomolecular simulation. Interoperability across different showcased through protein Molecular Dynamics setup transversal workflow, built using this run 5...
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation the possibility inspect intermediate results versatile graphical charts data visualization is very helpful, especially iterative processes, where parameters might adjusted a particular system of interest. This work presents collection...
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between different simulation and analysis tools. Moreover, need execute pipelines on distributed systems increases complexity of these developments. To address issues, we propose a methodology simplify implementation HPC infrastructures. combines library, BioExcel Building Blocks (BioBBs), that allows scientists implement as Python scripts, PyCOMPSs...
Mutations in the kinase domain of epidermal growth factor receptor (EGFR) can be drivers cancer and also trigger drug resistance patients receiving chemotherapy treatment based on inhibitors. A priori knowledge impact EGFR variants sensitivity would help to optimize design new drugs that are effective against resistant before they emerge clinical trials. To this end, we explored a variety silico methods, from sequence-based "state-of-the-art" atomistic simulations. We did not find any...
The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top common biomolecular simulation and bioinformatics tools. possibility to access the remotely programmatically increases its usability, allowing individual sporadic executions enabling remote workflows.BioBB REST API extends complements BioBB offering programmatic tools included in library. Molecular Dynamics setup, docking, structure modeling, free energy simulations flexibility analyses are examples...
ABSTRACT Mutations in the kinase domain of Epidermal Growth Factor Receptor (EGFR) can be drivers cancer and also trigger drug resistance patients under chemotherapy treatment based on inhibitors use. A priori knowledge impact EGFR variants sensitivity would help to optimize design new drugs effective against resistant variants. To this end, we have explored a variety silico methods, from sequence-based ‘state-of-the-art’ atomistic simulations. We did not find any sequence signal that...
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between different simulation and analysis tools. Moreover, need execute pipelines on distributed systems increases complexity of these developments. To address issues, we propose a methodology simplify implementation HPC infrastructures. combines library, BioExcel Building Blocks (BioBBs), that allows scientists implement as Python scripts, PyCOMPSs...
Abstract The usage of workflows has led to progress in many fields science, where the need process large amounts data is coupled with difficulty accessing and efficiently using High Performance Computing platforms. On one hand, scientists are focused on their problem concerned how data. top that, applications typically have different parts use tools for each part, thus complicating distribution reproducibility simulations. other computer concentrate develop frameworks deployment HPC or HTC...