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Internships initiative of the ISCB Student Council

Noura Chelbat, Avinash Kumar Shanmugam, Venkata P. Satagopam
2010 EMBnet journal  
doi:10.14806/ej.16.1.194 fatcat:lofpp2gr35hpvp37u6zjqg7qxa

Road to effective data curation for translational research

Wei Gu, Samiul Hasan, Philippe Rocca-Serra, Venkata P. Satagopam
2020 Drug Discovery Today  
Translational research today is data-intensive and requires multi-stakeholder collaborations to generate and pool data together for integrated analysis. This leads to the challenge of harmonization of data from different sources with different formats and standards, which is often overlooked during project planning and thus becomes a bottleneck of the research progress. We report on our experience and lessons learnt about data curation for translational research garnered over the course of the
more » ... TRIKS program (https://www.etriks.org), a unique, 5-year, cross-organizational, cross-cultural collaboration project funded by the Innovative Medicines Initiative of the EU. Here, we discuss the obstacles and suggest what steps are needed for effective data curation in translational research, especially for projects involving multiple organizations from academia and industry.
doi:10.1016/j.drudis.2020.12.007 pmid:33338655 fatcat:bo4ld4x5gvdfzkg5wofiv5gb6q

Arena3D: visualization of biological networks in 3D

Georgios A Pavlopoulos, Seán I O'Donoghue, Venkata P Satagopam, Theodoros G Soldatos, Evangelos Pafilis, Reinhard Schneider
2008 BMC Systems Biology  
Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results: We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data -such as proteins, chemicals, or pathways -can be grouped onto separate layers and arranged via layout
more » ... , such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion: Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from http://arena3d.org. Java3D library and Java 1.5 need to be pre-installed for the software to run.
doi:10.1186/1752-0509-2-104 pmid:19040715 pmcid:PMC2637860 fatcat:c266kh2bsrcs5a232xvbznqbcm

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets [article]

Miroslav Kratochvíl, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiří Vondrášek, Venkata P. Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
2020 bioRxiv   pre-print
AbstractBackgroundThe amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow to easily generate data with hundreds of millions of single-cell data points with more than 40 parameters, originating from thousands of individual samples. The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources. Current software
more » ... ools often do not scale to the datasets of such size; users are thus forced to down-sample the data to bearable sizes, in turn losing accuracy and ability to detect many underlying complex phenomena.ResultsWe present GigaSOM.jl, a fast and scalable implementation of clustering and dimensionality-reduction for flow and mass cytometry data. The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community, and allows for efficient handling and processing of datasets with billions of data points using distributed computing infrastructures. We describe the design of GigaSOM.jl, measure its performance and horizontal scaling capability, and showcase the functionality on a large dataset from a recent study.ConclusionsGigaSOM.jl facilitates utilization of the commonly available high-performance computing resources to process the largest available datasets within minutes, while producing results of the same quality as the current state-of-art software. Measurements indicate that the performance scales to much larger datasets. The example use on the data from an massive mouse phenotyping effort confirms the applicability of GigaSOM.jl to huge-scale studies.Key pointsGigaSOM.jl improves the applicability of FlowSOM-style single-cell cytometry data analysis by increasing the acceptable dataset size to billions of single cells.Significant speedup over current methods is achieved by distributed processing and utilization of efficient algorithms.GigaSOM.jl package includes support for fast visualization of multidimensional data.
doi:10.1101/2020.08.03.234187 fatcat:ecbke3gxljhvhfgtgcba4j7iaq

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software [article]

Laurent Heirendt and Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M.T. Fleming
2017 arXiv   pre-print
./ m a t l a b -n o d e s k t o p -n o s p l a s h < test / t e s t A test, part of the continuous integration test suite, is tailored to run a function in the /src directory such that a result is output  ...  The continuous integration infrastructure r i p t : # l a u n c h the t e s t s -bash . ci / r u n t e s t s . sh Fig. S2 .  ... 
arXiv:1712.05236v1 fatcat:w52xld7bqbfgnjcmu54qua2x3i

COBREXA.jl: constraint-based reconstruction and exascale analysis [article]

Miroslav Kratochvil, Laurent Heirendt, St. Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P. Satagopam, Oliver Ebenhoeh, Reinhard Schneider, Christophe Trefois, Wei Gu
2021 bioRxiv   pre-print
COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate its scalability by benchmarking the task distribution overhead incurred when performing analyses of
more » ... any variants of multi-organism community models simultaneously.
doi:10.1101/2021.06.04.447038 fatcat:eizxeoqsqbejdenooygvo5zyfi

Martini: using literature keywords to compare gene sets

Theodoros G. Soldatos, Seán I. O'Donoghue, Venkata P. Satagopam, Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, Reinhard Schneider
2009 Nucleic Acids Research  
The Fisher p-value for each keyword was then adjusted using: Adjusted p ¼ min p  n=k, 1 ð Þ where n is the total number of entities in a set, and k is the rank of the largest p-value that satisfies the  ...  By default, Martini returns only those keywords for which the adjusted p-value is <5%. However, Martini also provides users access to all keywords found, including those with higher p-value.  ... 
doi:10.1093/nar/gkp876 pmid:19858102 pmcid:PMC2800231 fatcat:i2u2r5cp5nezbbanfit54xxlla

Confronting the catalytic dark matter encoded by sequenced genomes

Kenneth W. Ellens, Nils Christian, Charandeep Singh, Venkata P. Satagopam, Patrick May, Carole L. Linster
2017 Nucleic Acids Research  
Paul P. Jung for critical reading of the manuscript and Prof. Rudi Balling for helpful comments.  ...  It remains unclear how ribitol-5-P, the substrate of ISPD for CDPribitol formation, is produced in human cells, leaving room for another enzyme identification in primary metabolism.  ...  (93) to identify a bacterial carbohydrate kinase domain containing protein of unknown function as an ATP/ADP-dependent NAD(P)H-hydrate dehydratase, a discovery made independently by Marbaix et al.  ... 
doi:10.1093/nar/gkx937 pmid:29059321 pmcid:PMC5714238 fatcat:oya4agqq6fbv3kfirizk4cjr6u

Reflect: A Practical Approach to Web Semantics

Seán I. O'Donoghue, Heiko Horn, Evangelos Pafilis, Sven Haag, Michael Kuhn, Venkata P. Satagopam, Reinhard Schneider, Lars J. Jensen
2010 Social Science Research Network  
To date, adding semantic capabilities to web content usually requires considerable server-side reengineering, thus only a tiny fraction of all web content currently has semantic annotations. Recently, we announced Reflect (http://reflect.ws), a free service that takes a more practical approach: Reflect uses augmented browsing to allow end-users to add systematic semantic annotations to any web-page in real-time, typically within seconds. In this paper we describe the tagging process in detail
more » ... d show how further entity types can be added to Reflect; we also describe how publishers and content providers can access Reflect programmatically using SOAP, REST (HTTP post), and JavaScript. Usage of Reflect has grown rapidly within the life sciences, and while currently only genes, protein and small molecule names are tagged, we plan to soon expand the scope to include a much broader range of terms (e.g., Wikipedia entries). The popularity of Reflect demonstrates the use and feasibility of letting end-users decide how and when to add semantic annotations. Ultimately, 'semantics is in the eye of the end-user', hence we believe end-user approaches such as Reflect will become increasingly important in semantic web technologies.
doi:10.2139/ssrn.3199471 fatcat:r643umqoq5gkvejctohg7rmjw4

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets

Miroslav Kratochvíl, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiří Vondrášek, Venkata P Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
2020 GigaScience  
The amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow the easy generation of data with hundreds of millions of single-cell data points with >40 parameters, originating from thousands of individual samples. The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources. Current software tools often do not
more » ... to the datasets of such size; users are thus forced to downsample the data to bearable sizes, in turn losing accuracy and ability to detect many underlying complex phenomena. We present GigaSOM.jl, a fast and scalable implementation of clustering and dimensionality reduction for flow and mass cytometry data. The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community and allows for efficient handling and processing of datasets with billions of data points using distributed computing infrastructures. We describe the design of GigaSOM.jl, measure its performance and horizontal scaling capability, and showcase the functionality on a large dataset from a recent study. GigaSOM.jl facilitates the use of commonly available high-performance computing resources to process the largest available datasets within minutes, while producing results of the same quality as the current state-of-art software. Measurements indicate that the performance scales to much larger datasets. The example use on the data from a massive mouse phenotyping effort confirms the applicability of GigaSOM.jl to huge-scale studies.
doi:10.1093/gigascience/giaa127 pmid:33205814 pmcid:PMC7672468 fatcat:dxbbboqj2jerxacuczpao37boy

nala: text mining natural language mutation mentions

Juan Miguel Cejuela, Aleksandar Bojchevski, Carsten Uhlig, Rustem Bekmukhametov, Sanjeev Kumar Karn, Shpend Mahmuti, Ashish Baghudana, Ankit Dubey, Venkata P Satagopam, Burkhard Rost, Jonathan Wren
2017 Bioinformatics  
P ¼ exact as in 'Tyr838 mutation' or 'Del 1473-IVS16(þ2)' and P ¼ vague as in 'placed immediately downstream of I444' or 'at the carboxyl end'.  ...  We annotated two cases: (1) W ¼ yes, L ¼ yes, P ¼ yesjvague, e.g.  ... 
doi:10.1093/bioinformatics/btx083 pmid:28200120 pmcid:PMC5870606 fatcat:ivlplahvmredpnjoeqvpstmszu

Caipirini: using gene sets to rank literature

Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Carolina Wanderley-Nogueira, Nina Mota Soares-Cavalcanti, Reinhard Schneider
2012 BioData Mining  
Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (http://
more » ... g) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes. Results: To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in Arabidopsis thaliana. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets. Conclusions: To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.
doi:10.1186/1756-0381-5-1 pmid:22297131 pmcid:PMC3307494 fatcat:23kojsxtwnbxlmdv6izswjdhsm

Reflect: A practical approach to web semantics

Seán I. O'Donoghue, Heiko Horn, Evangelos Pafilis, Sven Haag, Michael Kuhn, Venkata P. Satagopam, Reinhard Schneider, Lars J. Jensen
2010 Journal of Web Semantics  
To date, adding semantic capabilities to web content usually requires considerable server-side reengineering, thus only a tiny fraction of all web content currently has semantic annotations. Recently, we announced Reflect (http://reflect.ws), a free service that takes a more practical approach: Reflect uses augmented browsing to allow end-users to add systematic semantic annotations to any web-page in real-time, typically within seconds. In this paper we describe the tagging process in detail
more » ... d show how further entity types can be added to Reflect; we also describe how publishers and content providers can access Reflect programmatically using SOAP, REST (HTTP post), and JavaScript. Usage of Reflect has grown rapidly within the life sciences, and while currently only genes, protein and small molecule names are tagged, we plan to soon expand the scope to include a much broader range of terms (e.g., Wikipedia entries). The popularity of Reflect demonstrates the use and feasibility of letting end-users decide how and when to add semantic annotations. Ultimately, 'semantics is in the eye of the end-user', hence we believe end-user approaches such as Reflect will become increasingly important in semantic web technologies.
doi:10.1016/j.websem.2010.03.003 fatcat:v6ty5x5xpjfb3ghord7gtulsxa

Transcriptional Mechanisms Underlying Sensitization of Peripheral Sensory Neurons by Granulocyte-/Granulocyte-Macrophage Colony Stimulating Factors

Kiran Kumar Bali, Varun Venkataramani, Venkata P Satagopam, Pooja Gupta, Reinhard Schneider, Rohini Kuner
2013 Molecular Pain  
Gene pool with fold-change between +4 and −4 as compared to control-treated sensory neurons and P-BH < 0.05 (t-test, P with Benjamini and Hochberg False Discovery Rate < 0.05).  ...  < 0.05 (t-test, P with Benjamini and Hochberg False Discovery Rate < 0.05).  ... 
doi:10.1186/1744-8069-9-48 pmid:24067145 pmcid:PMC3852053 fatcat:zsn6xyd6ofhahcmh2ba75pujty

Genome-wide identification and functional analyses of microRNA signatures associated with cancer pain

Kiran Kumar Bali, Deepitha Selvaraj, Venkata P. Satagopam, Jianning Lu, Reinhard Schneider, Rohini Kuner
2013 EMBO Molecular Medicine  
à denotes p < 0.001 from PID-4 through 15 as compared to basal and † denotes p ¼ 0.004 on PID-5, 6 & 13, 0.006 on PID-7, 9 & 11, 0.005 on PID-8, 0.004 on PID-10, 0.0001 on PID-12 & 14, and 0.003 on PID  ...  à denotes p ¼ 0.002 on PID-5, 6, 7 and <0.0001 from PID-8 through 15 as compared to basal and † denotes p < 0.001 on PID-5 and <0.0001 from PID-6 through 15 as compared to corresponding data point in the  ...  à denotes p <:0.0001 as compared to mismatch-inhibitor group. B.  ... 
doi:10.1002/emmm.201302797 pmid:24039159 pmcid:PMC3840489 fatcat:f4fqonmz6vcbzipegbk6digeae
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