OligoPrime: An Information System for Oligonucleotide Management. (September 2021)

• Record Type: Journal Article
• Authors: Ravnik, Šimen; Žabkar, Ines; Prosenc Zmrzljak, Uršula; Jovčevska, Ivana; Šamec, Neja; Moškon, Miha; Videtič Paska, Alja
• Is Part Of: Biomedical engineering and computational biology. Volume 12(2021)
• Publication Date: 2021-09
• Subjects: Oligonucleotide -- primer -- information system -- management -- computational support -- web application; Biomedical engineering -- Periodicals; Computational biology -- Periodicals; Biomedical Engineering; Computational Biology; Biomedical engineering; Computational biology; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 610.2805
• DOI: 10.1177/11795972211041983
• Languages: English
• ISSNs: 1179-5972

Abstract

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 athttps://github.com/OligoPrime . Moreover, an implementation of OligoPrime, which can be used for testing is available athttp://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.