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Requirements Analysis Document

Dylan Spalding, Helen Parkinson, Jordi Rambla, Niclas Jareborg, Abdulrahman Azab, Ilkka Lappalainen, Jeff Almaida-King, Alexander Senf, Saif Ur-Rehman
2016 Zenodo  
This document details the purpose, features, and expected interfaces for the complete EXCELERATE WP9 (Use Case D: ELIXIR framework for secure archiving, dissemination and analysis of human access-controlled data). It outlines the tasks the system will perform, the constraints under which it operates, and how it reacts in certain circumstances. This document is intended for stakeholders, designers and developers as well as users of the system, and derives from a joint analysis carried out with these groups.
doi:10.5281/zenodo.61414 fatcat:uqpycs5kwze57l4hc6efuq2jk4

Comparison of One-Class SVM and Two-Class SVM for Fold Recognition [chapter]

Alexander Senf, Xue-wen Chen, Anne Zhang
2006 Lecture Notes in Computer Science  
The best protein structure prediction results today are achieved by incorporating initial structural prediction using alignments to known protein structures. The performance of these algorithms directly depends on the quality and significance of the alignment results. Support Vector Machines (SVMs) have shown great potential in providing good alignment results in cases where very low similarities to known proteins exist. In this paper we propose the use of a one-class SVM to reduce the
more » ... onal resources required to perform SVM learning and classification. Experimental results show its efficiency compared to two-class SVM algorithms while producing results of similar accuracy.
doi:10.1007/11893257_16 fatcat:s5sr4zbsyjhrfbhkv2f2qwmw5q

D9.4 Report On Implementation Of Cloud Access And Secure User And Data Management

Dylan Spalding, Helen Parkinson, Jordi Rambla, Ilkka Lappalainen, Juha Tornroos, Alexander Senf, Thomas Keane
2018 Zenodo  
The primary goal of EXCELERATE WP9 is to build and enhance the infrastructure to enable sharing of controlled access human genetic and phenotype data across Europe. Molecular medicine is undergoing a paradigm shift as advances in high throughput DNA sequencing technology make it feasible to use genomics in clinical practice. One of the core goals for the ELIXIR Human data platform is to enable sharing of human genetic data for research, acknowledging that in the future much of this data is
more » ... y to come from healthcare initiatives. In the near future, we expect that the majority of genomic data for research will come from secondary reuse of healthcare data. However, healthcare is considered a national competence and data generated is unlikely to be shared as freely as research data. WP9 of EXCELERATE aims to build the fundamental building blocks needed to establish a federated infrastructure across the ELIXIR network for human data sharing. The European Genome-phenome Archive (EGA) is an ELIXIR core data resource for permanent secure archiving and sharing of all types of potentially identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA has been operational since 2008 at EMBL-EBI, and in 2012 became a federated resource with the CRG, Barcelona. In this deliverable, we report on the development of two key components in support of the establishment of an ELIXIR wide federated human data infrastructure: 1. Create robust and standardised data access APIs that support new data access patterns such as real-time integration into downstream resource portals, cloud platforms, and local repositories. 2. Robust systems for the management of data access rights across the ELIXIR resources.
doi:10.5281/zenodo.1452473 fatcat:kx7j2vujora47nkluvos75t6t4

Crypt4GH: a file format standard enabling native access to encrypted data

Alexander Senf, Robert Davies, Frédéric Haziza, John Marshall, Juan Troncoso-Pastoriza, Oliver Hofmann, Thomas M Keane
2021 Bioinformatics  
The majority of genome analysis tools and pipelines require data to be decrypted for access. This potentially leaves sensitive genetic data exposed, either because the unencrypted data is not removed after analysis, or because the data leaves traces on the permanent storage medium. We defined a file container specification enabling direct byte-level compatible random access to encrypted genetic data stored in community standards such as SAM/BAM/CRAM/VCF/BCF. By standardizing this format, we
more » ... how it can be added as a native file format to genomic libraries, enabling direct analysis of encrypted data without the need to create a decrypted copy. The Crypt4GH specification can be found at:
doi:10.1093/bioinformatics/btab087 pmid:33543751 pmcid:PMC8522443 fatcat:gyobb6jewramdozpl4xplokggi

htsget: a protocol for securely streaming genomic data

Jerome Kelleher, Mike Lin, C H Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y Gonzalez, David K Jackson, Aaron Kemp, John Marshall, Andrew Nowak (+5 others)
2018 Bioinformatics  
Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration.
doi:10.1093/bioinformatics/bty492 pmid:29931085 pmcid:PMC6298043 fatcat:slz7ksxtjffl5e7bnbfcj5t24m

Integration of EGA secure data access into Galaxy

Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer (+4 others)
2016 F1000Research  
Galaxy Dylan Spalding ( ), Sanne Abeln ( ) Corresponding authors: Hoogstrate Y, Zhang C, Senf A How to cite this article: et al.  ... 
doi:10.12688/f1000research.10221.1 pmid:28232859 pmcid:PMC5302147 fatcat:eufkxb7tcrdwnajjdioxfwjlpy

CORBEL Prototype implementation of distributed automated data access request, review and authorization and delivery systems

Mikael Linden, Jan-Willem Boiten, Melanie Courtot, Petr Holub, Gert-Jan van de Geijn, David van Enckevort, Ilkka Lappalainen, Tommi Nyrönen, Helen Parkinson, Robert Reihs, Alexander Senf, Dylan Spalding (+5 others)
2019 Zenodo  
This deliverable describes research infrastructures' prototypes for granting a researcher an authorisation to access research data encouraging secondary use of data that is already collected. This deliverable further describes prototypes for delivering the decision on the granted access rights to the environment that enforces access control. The goal of this deliverable is to document and disseminate existing approaches in contributing research infrastructures. The main use case in this
more » ... ble is that data access requires authorisation because of its sensitive nature, for instance, if it involves samples from humans. Alternatively, it is possible that the data per se is not sensitive and suited to become public but cannot be shared pending the publication of the research results or filing a patent application. These two use cases are complementary and can be covered by the same technical approaches. Since this deliverable focuses on accessing research data, access to other kinds of assets (such as, instruments, biological samples and computing capacity) is out of scope. Transfer of research data between datacentres (including legal considerations of cross-national transfers) is also not covered in this deliverable. This deliverable first presents the key concepts, then previous work in life sciences and beyond as well as within relevant standards bodies (in particular, Global Alliance for Genomics and Health). Finally eight prototype implementations are presented from the contributing research infrastructures, including ELIXIR services for registered and controlled access, BBMRI-ERIC's Colorectal cancer cohort and Negotiator, EGA's work on DUO, BBMRI-NL Podium, SOLVE-RD Analysis Sandbox and LifeCycle Federated cohort analysis using DataShield. Before data access authorisation and delivery can be carried out, a researcher needs to be identified and their identity authenticated to a sufficient level of assurance. Existing approaches to researcher authentication are described here to the extent necessary for [...]
doi:10.5281/zenodo.3238496 fatcat:laeaoxmtw5cjpb3cffa2c2jqhu

The meV XUV-RIXS facility at UE112-PGM1 of BESSY II

Karl Bauer, Jan-Simon Schmidt, Frank Eggenstein, Régis Decker, Kari Ruotsalainen, Annette Pietzsch, Thomas Blume, Chun-Yu Liu, Christian Weniger, Frank Siewert, Jana Buchheim, Grzegorz Gwalt (+9 others)
2022 Journal of Synchrotron Radiation  
The toroidal mirror M1 collimates the beam from the undulator in the vertical plane for the monochromator and focuses horizontally on the horizontal aperture (Follath & Senf, 1997; Follath et al., 1998  ...  to its variable c ff one can choose between high flux (c ff closer to 1), high energy resolution (c ff away from 1), efficient higherorder suppression or zero order for alignment purposes (Follath & Senf  ... 
doi:10.1107/s1600577522003551 pmid:35511024 pmcid:PMC9070711 fatcat:ysdaa7jlpzcafalm5mt6lczsve

Content discovery and retrieval services at the European Nucleotide Archive

Nicole Silvester, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu (+12 others)
2014 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its discoverability and usability. In response to this, ENA has been introducing and improving checklists for use during submission and expanding its search facilities to provide targeted
more » ... search results. Here, we give a brief update on ENA content and some major developments undertaken in data submission services during 2014. We then describe in more detail the services we offer for data discovery and retrieval.
doi:10.1093/nar/gku1129 pmid:25404130 pmcid:PMC4383942 fatcat:7em6pbntxjbqdcs5xprtjkfwza

Psychooncological care for patients with cancer during twelve months of the Covid‐19 pandemic: Views and experiences of senior psychooncologists at German Comprehensive Cancer Centers

Andreas Dinkel, Ute Goerling, Klaus Hönig, André Karger, Imad Maatouk, Andrea Petermann‐Meyer, Bianca Senf, Katharina Woellert, Alexander Wünsch, Tanja Zimmermann, Frank Schulz‐Kindermann
2021 Psycho-Oncology  
� A monthly videoconference was maintained over 1 year, allowing senior psychooncologists from German Comprehensive Cancer Centers to discuss the implications of the Covid-19 pandemic for psychooncological care. � In the early phase of the pandemic, a widespread disruption of psychooncological services was noted. � Rapidly developed adaptations of regular services worked well and sometimes brought about unexpected, creative solutions.
doi:10.1002/pon.5759 pmid:34184361 pmcid:PMC8420502 fatcat:uh5d7civebeqvhpik3ik4lmhdi

Assembly information services in the European Nucleotide Archive

Nima Pakseresht, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li (+18 others)
2013 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many
more » ... ncements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.
doi:10.1093/nar/gkt1082 pmid:24214989 pmcid:PMC3965037 fatcat:sddhoeztgfdkhbyx3zrms3ajza

Facing growth in the European Nucleotide Archive

Guy Cochrane, Blaise Alako, Clara Amid, Lawrence Bower, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Mikyung Jang, Simon Kay, Rasko Leinonen, Xiu Lin (+17 others)
2012 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. collects, maintains and presents comprehensive nucleic acid sequence and related information as part of the permanent public scientific record. Here, we provide brief updates on ENA content developments and major service enhancements in 2012 and describe in more detail two important areas of development and policy that are driven by ongoing growth in sequencing technologies. First, we describe the ENA data warehouse, a resource
more » ... r which we provide a programmatic entry point to integrated content across the breadth of ENA. Second, we detail our plans for the deployment of CRAM data compression technology in ENA.
doi:10.1093/nar/gks1175 pmid:23203883 pmcid:PMC3531187 fatcat:fdf5xomwnbdz3kiv3ngyh44dty

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe (+14 others)
2017 F1000Research  
& Editing; : Investigation, van Enckevort D Hoogstrate Y Methodology, Software, Validation, Visualization, Writing -Review & Editing; : Investigation, Methodology, Resources, Writing -Review & Senf  ... 
doi:10.12688/f1000research.12168.1 pmid:29123641 pmcid:PMC5657030 fatcat:pmccjyaoffbmfd4rdcreqnx7je

The European Genome-phenome Archive of human data consented for biomedical research

Ilkka Lappalainen, Jeff Almeida-King, Vasudev Kumanduri, Alexander Senf, John Dylan Spalding, Saif ur-Rehman, Gary Saunders, Jag Kandasamy, Mario Caccamo, Rasko Leinonen, Brendan Vaughan, Thomas Laurent (+14 others)
2015 Nature Genetics  
doi:10.1038/ng.3312 pmid:26111507 pmcid:PMC5426533 fatcat:wmrsuwoqjreylbnu27sparqdai

Design and synthesis of photoswitchable polymerization catalysts [article]

Antti Alexander Senf, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
Senf, S. Hecht, Chem. Soc. Rev. 2014, 43, 1982-1996.  ...  Senf, S. Hecht, Chem. Soc. Rev. 2014, 43, 1982-1996. undergo an irreversible or a reversible photoreaction.  ... 
doi:10.18452/17544 fatcat:j2wkgqlgcjh53fsiz4neivwzfq
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