2019 |
Arvanitidis, Christos; Hollingsworth, Peter; Mergen, Patricia; Semal, Patrick; Keklikoglou, Kleoniki; Chatzinikolaou, Eva; Addnik, Wouter; Smith, Vincent; Koureas, Dimitrios Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project Journal Article Biodiversity Information Science and Standards, 3 , pp. e37290, 2019. Abstract | Links | BibTeX | Tags: DiSCCo, high-throughput imaging, high-throughput sequencing, LifeWatch ERIC, research infrastructures, SYNTHESYS+, virtual laboratories (vLabs), virtual research environments (VREs) @article{10.3897/biss.3.37290, title = {Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project}, author = {Christos Arvanitidis and Peter Hollingsworth and Patricia Mergen and Patrick Semal and Kleoniki Keklikoglou and Eva Chatzinikolaou and Wouter Addnik and Vincent Smith and Dimitrios Koureas}, url = {https://doi.org/10.3897/biss.3.37290}, doi = {10.3897/biss.3.37290}, year = {2019}, date = {2019-01-01}, journal = {Biodiversity Information Science and Standards}, volume = {3}, pages = {e37290}, publisher = {Pensoft Publishers}, abstract = {Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information you need into a digitized form of the physical objects, you can reach from the screen of your laptop, tablet or cell phone. You dream you were able to watch, inspect and even dissect the type material you need online but also to compare it with others they way sequences are blasted against large databases, these days. You plan to make global research on this taxon and try to derive patterns from both the molecular and organismal level of the biological organization and to link the patterns resulting to the drivers of change for this taxon. This is the vision of the Virtual Museum of Natural History and one of the ways to achieve this vision is to address the “collections on demand” requirement. One of the possible means to address this requirement is the digitization through the use of the micro-ct technology. The micro-CT virtual laboratory (vLab), developed by LifeWatchGreece research infrastructure (RI), makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. This presentation shows the development of such a “collections on demand” function, implemented by the SYNTHESYS+ project (DiSSCo RI), which combines such high-throughput technologies, that is micro-ct and genomics, to address the scientific community’s requirements. We show that this approach to combine patterns deriving from the application of novel techniques, which represent different kinds of observations is possible and we propose certain case studies as examples. The innovation aspects of this function include: Expansion and development of cost models for Collections on Demand; Development of standards and guidelines for exchange of collection-derived imaging data; Construction of new data pipelines and standard workflows, enabling access to complex digital content such as 3D scans; Development of novel molecular lab protocols, workflows and informatics pipelines, to enable large scale; DNA sequencing of NH collections.}, keywords = {DiSCCo, high-throughput imaging, high-throughput sequencing, LifeWatch ERIC, research infrastructures, SYNTHESYS+, virtual laboratories (vLabs), virtual research environments (VREs)}, pubstate = {published}, tppubtype = {article} } Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information you need into a digitized form of the physical objects, you can reach from the screen of your laptop, tablet or cell phone. You dream you were able to watch, inspect and even dissect the type material you need online but also to compare it with others they way sequences are blasted against large databases, these days. You plan to make global research on this taxon and try to derive patterns from both the molecular and organismal level of the biological organization and to link the patterns resulting to the drivers of change for this taxon. This is the vision of the Virtual Museum of Natural History and one of the ways to achieve this vision is to address the “collections on demand” requirement. One of the possible means to address this requirement is the digitization through the use of the micro-ct technology. The micro-CT virtual laboratory (vLab), developed by LifeWatchGreece research infrastructure (RI), makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. This presentation shows the development of such a “collections on demand” function, implemented by the SYNTHESYS+ project (DiSSCo RI), which combines such high-throughput technologies, that is micro-ct and genomics, to address the scientific community’s requirements. We show that this approach to combine patterns deriving from the application of novel techniques, which represent different kinds of observations is possible and we propose certain case studies as examples. The innovation aspects of this function include: Expansion and development of cost models for Collections on Demand; Development of standards and guidelines for exchange of collection-derived imaging data; Construction of new data pipelines and standard workflows, enabling access to complex digital content such as 3D scans; Development of novel molecular lab protocols, workflows and informatics pipelines, to enable large scale; DNA sequencing of NH collections. |
Knapp, Sandra; Vincent, Sarah; Arvanitidis, Christos; Dixey, Katherine; Mergen, Patricia Access to Natural History Collections – from SYNTHESYS to DiSSCo Journal Article Biodiversity Information Science and Standards, 3 , pp. e37149, 2019. Abstract | Links | BibTeX | Tags: access, collections, DiSSCo, physical access, SYNTHESYS+, virtual access @article{10.3897/biss.3.37149, title = {Access to Natural History Collections – from SYNTHESYS to DiSSCo}, author = {Sandra Knapp and Sarah Vincent and Christos Arvanitidis and Katherine Dixey and Patricia Mergen}, url = {https://doi.org/10.3897/biss.3.37149}, doi = {10.3897/biss.3.37149}, year = {2019}, date = {2019-01-01}, journal = {Biodiversity Information Science and Standards}, volume = {3}, pages = {e37149}, publisher = {Pensoft Publishers}, abstract = {Any one collection of objects never tells the whole story. Enabling access to natural history collections by users external to a given institution, has a long history–even that great stay-at-home, Linnaeus, relied on specimens in the hands of others. Neglecting collections outside one’s institution results in duplication and inefficiency, as can be seen in the history of synonymy. Physical access had always been the norm, but difficult for the single individual. A student in the late 20th century had to decide if money were better spent going to one collection or another, or if the sometimes rather fuzzy photographs really represented the taxon she was working with. Loans between institutions were a way to provide access, but came with their own risks. The very individualised–to users as well as institutions–system of access provisioning still operates today but has fundamentally changed in several respects. The SYNTHESYS (Synthesis of Systematic Resources) projects brought a set of European institutions into a consortium with one aim: to provide access to natural history collections in order to stimulate their use across communities. The SYNTHESYS Transnational Access (TA) programme provided access not only to the collections of participating institutions, but also to infrastructures such as laboratories and analytical facilities. The trajectory of TA has led to a change in thinking about natural history collections, along with access to them. Because access has been subsidised at both the individual and institutional levels, participating institutions began to function more as a collective; one infrastructure, albeit loosely dispersed. In the most recent iteration of the SYNTHESYS programme, SYNTHESYS+, access has changed yet again with the times. Technological advances in imaging permit high-quality surrogates of natural history specimens to be exchanged more freely, and Virtual Access (VA) forms an integral part of the SYNTHESYS+ access programme, alongside TA. Virtual access has been operating for some time in the natural history collections community, but like TA, with individual scientists requesting images/sequences/scans from individual institutions or curators. VA, as a centralised service, will be piloted in SYNTHESYS+ in order to establish the basis for community change in access provisioning. But what next? Will we continue to need physical access to specimens and facilities as VA becomes increasingly feasible? As European collections-based institutions coalesce into the DiSSCo (Distributed System of Systematics Collections) infrastructure, will the model established in SYNTHESYS+ continue to function in the absence of centralised funding? In this talk, we will explore the trajectory of access through SYNTHESYS and provide some scenarios for how access to natural history collections–both physical and virtual–may change as we transition to the broader infrastructure that DiSSCo represents.}, keywords = {access, collections, DiSSCo, physical access, SYNTHESYS+, virtual access}, pubstate = {published}, tppubtype = {article} } Any one collection of objects never tells the whole story. Enabling access to natural history collections by users external to a given institution, has a long history–even that great stay-at-home, Linnaeus, relied on specimens in the hands of others. Neglecting collections outside one’s institution results in duplication and inefficiency, as can be seen in the history of synonymy. Physical access had always been the norm, but difficult for the single individual. A student in the late 20th century had to decide if money were better spent going to one collection or another, or if the sometimes rather fuzzy photographs really represented the taxon she was working with. Loans between institutions were a way to provide access, but came with their own risks. The very individualised–to users as well as institutions–system of access provisioning still operates today but has fundamentally changed in several respects. The SYNTHESYS (Synthesis of Systematic Resources) projects brought a set of European institutions into a consortium with one aim: to provide access to natural history collections in order to stimulate their use across communities. The SYNTHESYS Transnational Access (TA) programme provided access not only to the collections of participating institutions, but also to infrastructures such as laboratories and analytical facilities. The trajectory of TA has led to a change in thinking about natural history collections, along with access to them. Because access has been subsidised at both the individual and institutional levels, participating institutions began to function more as a collective; one infrastructure, albeit loosely dispersed. In the most recent iteration of the SYNTHESYS programme, SYNTHESYS+, access has changed yet again with the times. Technological advances in imaging permit high-quality surrogates of natural history specimens to be exchanged more freely, and Virtual Access (VA) forms an integral part of the SYNTHESYS+ access programme, alongside TA. Virtual access has been operating for some time in the natural history collections community, but like TA, with individual scientists requesting images/sequences/scans from individual institutions or curators. VA, as a centralised service, will be piloted in SYNTHESYS+ in order to establish the basis for community change in access provisioning. But what next? Will we continue to need physical access to specimens and facilities as VA becomes increasingly feasible? As European collections-based institutions coalesce into the DiSSCo (Distributed System of Systematics Collections) infrastructure, will the model established in SYNTHESYS+ continue to function in the absence of centralised funding? In this talk, we will explore the trajectory of access through SYNTHESYS and provide some scenarios for how access to natural history collections–both physical and virtual–may change as we transition to the broader infrastructure that DiSSCo represents. |
ResearchGate Link : https://www.researchgate.net/project/MOBILISE-COST-Action-CA17106-Mobilising-Data-Policies-and-Experts-in-Scientific-Collections