OligoPrime : an information system for oligonucleotide management

Ravnik, Šimen (author), Žabkar, Ines (author), Prosenc Zmrzljak, Uršula (author), Jovchevska, Ivana (author), Šamec, Neja (author), Moškon, Miha (author), Videtič Paska, Alja (author)

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.

• Language: English
• Keywords: oligonucleotide, primer, information system, management, computational support, web application
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FRI - Faculty of Computer and Information Science ; MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 9 str.
• Numbering: Vol. 12
• PID: 20.500.12556/RUL-144163
• UDC: 004:577
• ISSN on article: 1179-5972
• DOI: 10.1177/11795972211041983
• COBISS.SI-ID: 75739139
• Publication date in RUL: 02.02.2023

RAVNIK, Šimen, ŽABKAR, Ines, PROSENC ZMRZLJAK, Uršula, JOVCHEVSKA, Ivana, ŠAMEC, Neja, MOŠKON, Miha and VIDETIČ PASKA, Alja, 2021, OligoPrime : an information system for oligonucleotide management. Biomedical engineering and computational biology [online]. 2021. Vol. 12. [Accessed 7 April 2025]. DOI 10.1177/11795972211041983. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=144163

Record is a part of a journal

• Title: Biomedical engineering and computational biology
• Shortened title: Biomed. eng. comput. biol.
• Publisher: SAGE
• ISSN: 1179-5972
• COBISS.SI-ID: 523005721

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: oligonukleotid, oligonukleotidni začetnik, informacijski sistem, vodenje, računalniška podpora, spletna aplikacija