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OligoPrime: An Information System for Oligonucleotide Management

With the increasing number of molecular biology techniques, large numbers of oligonucleotides are frequently involved in individual research projects. Thus, a dedicated electronic oligonucleotide management system is expected to provide several benefits such as increased oligonucleotide traceability...

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Autores principales: Ravnik, Šimen, Žabkar, Ines, Prosenc Zmrzljak, Uršula, Jovčevska, Ivana, Šamec, Neja, Moškon, Miha, Videtič Paska, Alja
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442484/
https://www.ncbi.nlm.nih.gov/pubmed/34539193
http://dx.doi.org/10.1177/11795972211041983
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author Ravnik, Šimen
Žabkar, Ines
Prosenc Zmrzljak, Uršula
Jovčevska, Ivana
Šamec, Neja
Moškon, Miha
Videtič Paska, Alja
author_facet Ravnik, Šimen
Žabkar, Ines
Prosenc Zmrzljak, Uršula
Jovčevska, Ivana
Šamec, Neja
Moškon, Miha
Videtič Paska, Alja
author_sort Ravnik, Šimen
collection PubMed
description With the increasing number of molecular biology techniques, large numbers of oligonucleotides are frequently involved in individual research projects. Thus, a dedicated electronic oligonucleotide management system is expected to provide several benefits such as increased oligonucleotide traceability, facilitated sharing of oligonucleotides between laboratories, and simplified (bulk) ordering of oligonucleotides. Herein, we describe OligoPrime, an information system for oligonucleotide management, which presents a computational support for all steps in an oligonucleotide lifecycle, namely, from its ordering and storage to its application, and disposal. OligoPrime is easy to use since it is accessible via a web browser and does not require any installation from the end user’s perspective. It allows filtering and search of oligonucleotides by various parameters, which include the exact location of an oligonucleotide, its sequence, and availability. The oligonucleotide database behind the system is shared among the researchers working in the same laboratory or research group. Users might have different roles which define the access permissions and range from students to researchers and primary investigators. Furthermore, OligoPrime is easy to manage and install and is based on open-source software solutions. Its code is freely available at https://github.com/OligoPrime. Moreover, an implementation of OligoPrime, which can be used for testing is available at http://oligoprime.xyz/. To our knowledge, OligoPrime is the only software solution dedicated specifically to oligonucleotide management. We strongly believe that it has a large potential to enhance the transparency of use and to simplify the management of oligonucleotides in academic laboratories and research groups.
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spelling pubmed-84424842021-09-16 OligoPrime: An Information System for Oligonucleotide Management Ravnik, Šimen Žabkar, Ines Prosenc Zmrzljak, Uršula Jovčevska, Ivana Šamec, Neja Moškon, Miha Videtič Paska, Alja Biomed Eng Comput Biol Technical Advances With the increasing number of molecular biology techniques, large numbers of oligonucleotides are frequently involved in individual research projects. Thus, a dedicated electronic oligonucleotide management system is expected to provide several benefits such as increased oligonucleotide traceability, facilitated sharing of oligonucleotides between laboratories, and simplified (bulk) ordering of oligonucleotides. Herein, we describe OligoPrime, an information system for oligonucleotide management, which presents a computational support for all steps in an oligonucleotide lifecycle, namely, from its ordering and storage to its application, and disposal. OligoPrime is easy to use since it is accessible via a web browser and does not require any installation from the end user’s perspective. It allows filtering and search of oligonucleotides by various parameters, which include the exact location of an oligonucleotide, its sequence, and availability. The oligonucleotide database behind the system is shared among the researchers working in the same laboratory or research group. Users might have different roles which define the access permissions and range from students to researchers and primary investigators. Furthermore, OligoPrime is easy to manage and install and is based on open-source software solutions. Its code is freely available at https://github.com/OligoPrime. Moreover, an implementation of OligoPrime, which can be used for testing is available at http://oligoprime.xyz/. To our knowledge, OligoPrime is the only software solution dedicated specifically to oligonucleotide management. We strongly believe that it has a large potential to enhance the transparency of use and to simplify the management of oligonucleotides in academic laboratories and research groups. SAGE Publications 2021-09-08 /pmc/articles/PMC8442484/ /pubmed/34539193 http://dx.doi.org/10.1177/11795972211041983 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution 4.0 License (https://creativecommons.org/licenses/by/4.0/) which permits any use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Technical Advances
Ravnik, Šimen
Žabkar, Ines
Prosenc Zmrzljak, Uršula
Jovčevska, Ivana
Šamec, Neja
Moškon, Miha
Videtič Paska, Alja
OligoPrime: An Information System for Oligonucleotide Management
title OligoPrime: An Information System for Oligonucleotide Management
title_full OligoPrime: An Information System for Oligonucleotide Management
title_fullStr OligoPrime: An Information System for Oligonucleotide Management
title_full_unstemmed OligoPrime: An Information System for Oligonucleotide Management
title_short OligoPrime: An Information System for Oligonucleotide Management
title_sort oligoprime: an information system for oligonucleotide management
topic Technical Advances
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442484/
https://www.ncbi.nlm.nih.gov/pubmed/34539193
http://dx.doi.org/10.1177/11795972211041983
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