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euCanSHare. Deliverables D2.1 - Initial Infrastructure framework and documentation

Josep Lluís Gelpí, Laia Codó, Alejandro Canosa
2019 Zenodo  
euCanSHare deliverable D2.1 reporting on the initial infrastructure of the framework and documentation. Abstract: EuCanSHare aims to establish a unified environment for cardiovascular data sharing and analysis. The euCanSHare data platform will provide support for i) a unified Data Catalogue combining in a single site all data managed by the project; ii) a platform to manage data access credentials; iii) a computational platform that combines controlled access to data, analysis and
more » ... tools. This document describes the technological foundations of the euCanSHare data portal. It is a cloud-based environment providing the computational infrastructure for data management and analysis, an authentication and authorization system, and the necessary user interfaces. The document is organized as follows: Section 1 describes the motivation and overall strategy; section 2 summarizes the design of the infrastructure; software components are described in detail in section 3 and finally, section 4 outlines the development roadmap until the release of the first complete prototype (M24).
doi:10.5281/zenodo.3570347 fatcat:h6fw3nqrqfhzln2oiqzh5syc2a

FAIRsoft - A practical implementation of FAIR principles for research software [article]

Eva Martin del Pico, Josep Lluis Gelpi, Salvador Capella-Gutierrez
2022 bioRxiv   pre-print
Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is challenging to reproduce and verify most of the time. It could be undocumented, opaque, may even contain unknown errors that affect the outcome, or be directly unavailable, and impossible to use by others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software
more » ... the domain should meet to ensure its quality and sustainability, resembling the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles. Within the ELIXIR infrastructure, OpenEBench aims to be an open platform providing both support for scientific benchmarking and an active observatory of software quality for the universe of Life Sciences research software. We present our initial proposal to instantiate a FAIR-like framework for assessing software qualitythe first step toward the implementation of such an observatory in OpenEBench.
doi:10.1101/2022.05.04.490563 fatcat:2x5twlji65cp5mnmbqw4fpdnuy

Standards for data handling

Ramon Goñi, Rossen Apostolov, Magnus Lundborg, Christoph Bernau, Ferdinand Jamitzky, Erwin Laure, Erik Lindahl, Pau Andrio, Yolanda Becerra, Modesto Orozco, Josep Lluís Gelpí
2013 Zenodo  
We present in this paper ScalaLife's proposed data standards and best practices for Molecular Dynamics data management. Our proposed data standard is divided in two layers: the XML UMM format and the embedded TNG file. TNG is a high-compressed and robust file format that allows nonsequential access to trajectory information. TNG will be adopted by GROMACS from the next major release. UMM is implemented in XSD and sets the common definition of high-level simulation information. We also
more » ... d UMM-MoDEL, a database software bundle to manage MD simulation data using UMM/TNG standards. ScalaLife is working for the adoption of the standards developing open I/O APIs, converters and interfaces for Life Sciences community.
doi:10.5281/zenodo.4468929 fatcat:ryzdynn7erdejmijkzeqy3pnyu

Bioexcel Deliverable 2.3 - User Feedback And Future Roadmap

Adam Hospital, Josep Lluís Gelpí, Jose A. Dianes, Pau Andrio, Darren J. White, Emiliano Ippoliti, Adrien Melquiond, Vytautas Gapsys
2017 Zenodo  
The project, led by Josep Lluís Gelpí (BSC-ES) and Carole Goble (UNIMAN-UK) intends to put together recommendations for the registration and specification of bioinformatics tools and workflows, enabling  ... 
doi:10.5281/zenodo.1060946 fatcat:i4exxpnhpbaqnglrltelddzw6a

BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap

Adam Hospital, Stian Soiland-Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier
2019 Zenodo  
This deliverable is presented as a follow-up to the BioExcel-1 D2.1 deliverable, describing the new state of the art of technologies, methods and tools applicable to the computational biomolecular field, and presenting a roadmap for WP2 in the first period (18 months) of the BioExcel-2 project. A current situation section briefly summarizes the work done in BioExcel- 1 on the development of the BioExcel building blocks (biobb) library following a collection of software development best
more » ... , success stories reached for a set of workflows built using this library, and finding and using BioExcel workflows through the BioExcel Cloud Portal. The state of the art of technologies, tools and methods presented in the BioExcel-1 D2.1 is reviewed, briefly describing new hardware and software infrastructures that have been gaining popularity in the recent years, such as software containers or Jupyter notebooks. Workflow managers, especially the ones focused on the HPC and exascale supercomputers are also reviewed, presenting a collaboration with the Molecular Science Software Institute (MolSSI). New, still ongoing initiatives closely related to the BioExcel expertise are introduced, including workflows and MD trajectories data repositories. The set of available modules used on the solution-oriented workflows built for the first period of the project will be updated in this new period. A new list of proposed tools to be wrapped into the BioExcel building block library is presented, including advanced and modern functionalities such as biased MD simulations and High Performance Data Analytics (HPDA). The final section of the deliverable describes the immediate future roadmap for the WP2, divided in the different tasks presented in the DoA: Application building blocks for computational biomolecular simulations Definition, development and specification of workflow prototypes and demonstrators Optimization of Workflows for Exascale computing Convergence o [...]
doi:10.5281/zenodo.4604607 fatcat:u3yplgrepzfytda2zwzu37phge

Adenovirus-mediated wt- p16 reintroduction induces cell cycle arrest or apoptosis in pancreatic cancer

Joaquim Calbó, Mario Marotta, Manel Cascalló, Josep Maria Roig, Josep Lluis Gelpí, Juan Fueyo, Adela Mazo
2001 Cancer Gene Therapy  
Pancreatic cancer has long carried poor prognosis. The development of new therapeutic approaches is particularly urgent. Inactivation of the tumor -suppressor gene p16 INK4a / CDKN2 , a specific inhibitor of the cyclin -dependent kinases CDK4 and CDK6, is the most common genetic alteration in human pancreatic cancer, making it an ideal target for gene replacement. Here we transfected tumor cells using a recombinant adenovirus containing the wt -p16 cDNA ( Ad5RSV -p16 ). The overexpression of
more » ... decreased cell proliferation in all four human pancreatic tumor cell lines ( NP -9, NP -18, NP -29, and NP -31 ). However, G 1 arrest and senescence were observed in only three. In contrast, the fourth ( NP -18 ) showed a significant increase in apoptosis. This differential behavior may be related to the differences found in the expression level of E2F -1. Experiments on subcutaneous pancreatic xenografts demonstrated the effectiveness of p16 in the inhibition of pancreatic tumor growth in vivo. Taken together, our results indicate that approaches involving p16 replacement are promising in pancreatic cancer treatment. Cancer Gene Therapy ( 2001 ) 8, 740 -750
doi:10.1038/sj.cgt.7700374 pmid:11687897 fatcat:hatejdpqwnctzd7syq2zd2seke

Effects of Cadmium and Mercury on the Upper Part of Skeletal Muscle Glycolysis in Mice

Maria José Ramírez-Bajo, Pedro de Atauri, Fernando Ortega, Hans V. Westerhoff, Josep Lluis Gelpí, Josep J. Centelles, Marta Cascante, Fernando Rodrigues-Lima
2014 PLoS ONE  
The effects of pre-incubation with mercury (Hg 2+ ) and cadmium (Cd 2+ ) on the activities of individual glycolytic enzymes, on the flux and on internal metabolite concentrations of the upper part of glycolysis were investigated in mouse muscle extracts. In the range of metal concentrations analysed we found that only hexokinase and phosphofructokinase, the enzymes that shared the control of the flux, were inhibited by Hg 2+ and Cd 2+ . The concentrations of the internal metabolites
more » ... osphate and fructose-6-phosphate did not change significantly when Hg 2+ and Cd 2+ were added. A mathematical model was constructed to explore the mechanisms of inhibition of Hg 2+ and Cd 2+ on hexokinase and phosphofructokinase. Equations derived from detailed mechanistic models for each inhibition were fitted to the experimental data. In a concentration-dependent manner these equations describe the observed inhibition of enzyme activity. Under the conditions analysed, the integral model showed that the simultaneous inhibition of hexokinase and phosphofructokinase explains the observation that the concentrations of glucose-6-phosphate and fructose-6-phosphate did not change as the heavy metals decreased the glycolytic flux.
doi:10.1371/journal.pone.0080018 pmid:24489641 pmcid:PMC3904826 fatcat:25dm7swyd5e3pkgyal6py5527y

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking [article]

Salvador Capella-Gutierrez, Diana de la Iglesia, Juergen Haas, Analia Lourenco, Jose Maria Fernandez Gonzalez, Dmitry Repchevsky, Christophe Dessimoz, Torsten Schwede, Cedric Notredame, Josep Lluis Gelpi, Alfonso Valencia
2017 bioRxiv   pre-print
The dependence of life scientists on software has steadily grown in recent years. For many tasks, researchers have to decide which of the available bioinformatics software are more suitable for their specific needs. Additionally researchers should be able to objectively select the software that provides the highest accuracy, the best efficiency and the highest level of reproducibility when integrated in their research projects. Critical benchmarking of bioinformatics methods, tools and web
more » ... ces is therefore an essential community service, as well as a critical component of reproducibility efforts. Unbiased and objective evaluations are challenging to set up and can only be effective when built and implemented around community driven efforts, as demonstrated by the many ongoing community challenges in bioinformatics that followed the success of CASP. Community challenges bring the combined benefits of intense collaboration, transparency and standard harmonization. Only open systems for the continuous evaluation of methods offer a perfect complement to community challenges, offering to larger communities of users, that could extend far beyond the community of developers, a window to the developments status that they can use for their specific projects. We understand by continuous evaluation systems as those services which are always available and periodically update their data and/or metrics according to a predefined schedule keeping in mind that the performance has to be always seen in terms of each research domain. We argue here that technology is now mature to bring community driven benchmarking efforts to a higher level that should allow effective interoperability of benchmarks across related methods. New technological developments allow to overcome the limitations of the first experiences on online benchmarking e.g. EVA. We therefore describe OpenEBench, a novel infra-structure designed to establish a continuous automated benchmarking system for bioinformatics methods, tools and web services. OpenEBench is being developed so as to cater for the needs of the bioinformatics community, especially software developers who need an objective and quantitative way to inform their decisions as well as the larger community of end-users, in their search for unbiased and up-to-date evaluation of bioinformatics methods. As such OpenEBench should soon become a central place for bioinformatics software developers, community-driven benchmarking initiatives, researchers using bioinformatics methods, and funders interested in the result of methods evaluation.
doi:10.1101/181677 fatcat:5jiuva35g5fodd625vkqkfwefm

Obligatory Amino Acid Exchange via Systems bo,+-like and y+L-like

Josep Chillarón, Raúl Estévez, Conchi Mora, Carsten A. Wagner, Hartmut Suessbrich, Florian Lang, Josep Lluís Gelpí, Xavier Testar, Andreas E. Busch, Antonio Zorzano, Manuel Palacín
1996 Journal of Biological Chemistry  
Mutations in the rBAT gene cause type I cystinuria, a common inherited aminoaciduria of cystine and dibasic amino acids due to their defective renal and intestinal reabsorption (Calonge, M. A. 92, 9667-9671). One important question that remains to be clarified is how the apparently non-concentrative system b o,؉ -like, associated with rBAT expression, participates in the active renal reabsorption of these amino acids. Several studies have demonstrated exchange of amino acids induced by rBAT in
more » ... enopus oocytes. Here we offer evidence that system b o,؉ -like is an obligatory amino acid exchanger in oocytes and in the "renal proximal tubular" cell line OK. System b o,؉ -like showed a 1:1 stoichiometry of exchange, and the hetero-exchange dibasic (inward) with neutral (outward) amino acids were favored in oocytes. Obligatory exchange of amino acids via system b o,؉ -like fully explained the amino acid-induced current in rBAT-injected oocytes. Exchange via system b o,؉ -like is coupled enough to ensure a specific accumulation of substrates until the complete replacement of the internal oocyte substrates. Due to structural and functional analogies of the cell surface antigen 4F2hc to rBAT, we tested for amino acid exchange via system y ؉ L-like. 4F2hc-injected oocytes accumulated substrates to a level higher than CAT1-injected oocytes (i.e. oocytes expressing system y ؉ ) and showed exchange of amino acids with the substrate specificity of system
doi:10.1074/jbc.271.30.17761 pmid:8663357 fatcat:3o7ze2iuord27nkmjouytktgpm

NAFlex: a web server for the study of nucleic acid flexibility

Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluis Gelpí, Modesto Orozco
2013 Nucleic Acids Research  
We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a
more » ... y of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona. org/NAFlex webpage.
doi:10.1093/nar/gkt378 pmid:23685436 pmcid:PMC3692121 fatcat:rgzxoxlrffafpnieq2jxwozncm

BioExcel-2 Deliverable 2.2 – First release of workflow-ready building blocks library

Adam Hospital, Genís Bayarri, Stian Soiland- Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier, Rosa Maria Badia
2019 Zenodo  
This deliverable presents the first release of the workflow-ready BioExcel building blocks library for the BioExcel-2 period. The initial roadmap of the novel identified building blocks presented in D2.1 is revised, and a new, updated roadmap for the rest of the project is presented. The current situation section contains a description of the new release of the BioExcel building blocks library, including the content of the release, the new library modules recently developed, updates on the
more » ... dy existing modules, new functionalities and bug fixes, and work done into increasing its visibility and outreach. The initial and updated roadmap section contains a revision of the initial roadmap presented in the D2.1 document in PM6, highlighting the milestones reached and issues found. From that, an updated roadmap for the development of the software library during the next 2 years is proposed, including a large set of new building blocks.
doi:10.5281/zenodo.4605207 fatcat:efnlmp3u3rhkhfof7yyn67uk7i

Structural and energetic study of cation–π–cation interactions in proteins

Silvana Pinheiro, Ignacio Soteras, Josep Lluis Gelpí, François Dehez, Christophe Chipot, F. Javier Luque, Carles Curutchet
2017 Physical Chemistry, Chemical Physics - PCCP  
Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.
doi:10.1039/c6cp08448f pmid:28352893 fatcat:hfdr4ei4mbagdilz5tbmv5shw4

Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis

Adam Hospital, Anna Montras, Stian Soiland-Reyes, Alexandre Bonvin, Adrien Melquiond, Josep Lluís Gelpí, Daniele Lezzi, Steven Newhouse, Jose A. Dianes, Mark Abraham, Rossen Apostolov, Emiliano Ippoliti (+2 others)
2016 Zenodo  
This deliverable describes the state of the art and gives a technological gap analysis in the portable environments for computing and data resources of BioExcel. We review the commonly used technologies for computational infrastructures, a selection of workflow managers for computational biology and three important repositories for biomolecular data. We then provide a catalogue of tools that are supported by BioExcel partners, which will become the building blocks used in the pipelines and
more » ... versal workflow units of our pilot use cases. We then describe the seven BioExcel pilot use cases. To help identify potential issues in developing the corresponding pipelines, the use cases have been individually described and analyzed, focusing on the set of functionalities (from the tool catalogue and elsewhere) that form a complete workflow. Interoperability between building blocks and data models are explored using workflow diagrams. Finally, we summarize the technological gaps for each use case. We analyzed the user feedback from WP3 to highlight key focus areas for BioExcel's future work. From the initial WP3 survey together with previous HADDOCK and GROMACS surveys we identified three main areas of potential user interest: Interoperability, usability and remotely accessible tools. For the interoperability issue, we found that the need for manual interaction needs to be reduced, for instance by incorporating workflow managers to integrate processes and input/output data. For the usability part, we found that improvements could be made to the main codes (GROMACS, HADDOCK and CPMD) to ease their usage, such as web portals providing assistance on how to run, install or use advanced configuration options. Finally, we realized that a high number of users would be interested in using remote tools, although several concerns have been raised about this, namely data privacy, reliability, and lack of control. Based o [...]
doi:10.5281/zenodo.263963 fatcat:o2v7ogjmnbauhn7txp2buz3pem

Long-timescale dynamics of the Drew–Dickerson dodecamer

Pablo D. Dans, Linda Danilāne, Ivan Ivani, Tomáš Dršata, Filip Lankaš, Adam Hospital, Jürgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis Gelpí, Richard Lavery, Modesto Orozco
2016 Nucleic Acids Research  
We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC) 2 ) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na + Cl − or K + Cl − . The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10
more » ... simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
doi:10.1093/nar/gkw264 pmid:27084952 pmcid:PMC4872116 fatcat:zpfjtwjbvzcvjojme7rpqtc3wy

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, Modesto Orozco
2010 Structure  
For binding sites of known pharmacological targets the use of docking programs such as CMIP (Gelpí et al., 2001) , can yield potential structures of drug-protein complexes (see some examples in Figure  ...  can be downloaded, sent to additional tools either open like FlexServ (Camps et al., 2009) , or restricted like MDWeb (Hospital et al., to be published), MDGRID (Carrillo and Orozco, 2008) , CMIP (Gelpí  ... 
doi:10.1016/j.str.2010.07.013 pmid:21070939 fatcat:jyc64i63grap5hvenuwwjppvyu
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