Developing a Bioinformatics Program and Supporting Infrastructure in a Biomedical Library

Hosburgh, Nathan

doi:10.7191/jeslib.2018.1129

Cited by 6 publications

(2 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Medical Libraries have been providing bioinformatics services in support of biomedical research for several years. These programs usually include consultation services, training, collaborations, and networked biological information resources (Chattopadhyay et al, 2006;Li, Chen & Clintworth, 2013;Hosburgh, 2018). In 2014, the Harvey Cushing/John Hay Whitney Medical Library (CWML) at Yale University started a Bioinformatics Support Program (BSP) intended to support Yale University-affiliated biomedical researchers.…”

Section: Introductionmentioning

confidence: 99%

Peer Teaching as Bioinformatics Training Strategy: Incentives, Challenges, and Benefits

Rahman

Meyer

Thakral

et al. 2022

Medical Reference Services Quarterly

View full text Add to dashboard Cite

As biomedical research becomes more data-intensive, bioinformatics is becoming essential to understanding biological processes, systems, and diseases. In this paper we describe the use of a series of peer teaching workshops as a strategy to respond to the bioinformatics training needs at a research-intensive institution. In addition to the data collected from the workshops, we also used personal experiences of researchers who participated as peer teachers to understand the incentives, challenges, and benefits of peer teaching. Developing communication skills such as confidence in teaching, explaining complex concepts, and better understanding of the topic emerged as primary benefits that the teachers obtained from this experience. Lack of time for teaching and the struggles of classroom management were identified as two major challenges. We suggest that peer teaching can be beneficial not only to train researchers in bioinformatics, but also as a professional development opportunity for graduate students and postdoctoral trainees.

show abstract

Section: Introductionmentioning

confidence: 99%

Peer Teaching as Bioinformatics Training Strategy: Incentives, Challenges, and Benefits

Rahman

Meyer

Thakral

et al. 2022

Medical Reference Services Quarterly

View full text Add to dashboard Cite

show abstract

“…Bioinformatics is a scientific discipline that involves various fields of science, such as computing, mathematics, modern molecular biology, and medical research [1]. One application of bioinformatics is drug design, which is the search for a cavity (binding site) on a protein that acts as an attachment site for a ligand (small particle) or drug candidate.…”

Section: Introductionmentioning

confidence: 99%

Predicting Protein-Ligand Binding Site for Drug Design Using Context Relevant Self Organizing Maps (CRSOM)

Imah¹,

Wulandari²

2020

IJIES

View full text Add to dashboard Cite

Research on binding sites has been done to find suitable ligands to treat a particular disease. The binding site is a pocket on the surface of the protein, which acts as a place to attach a ligand. In bioinformatics, searching for binding sites is applied to drug design problems. Currently, computer-aided drug design has been developed. In this study, the prediction of protein-ligand binding sites formulated as a binary classification, which is distinguish the location that has potential to binding the ligand and the location that has no potential to binding the ligand. The dataset that will be used in this research is taken from the RCSB Protein Data Bank of 14 proteins data. The classification method used in this research is Context Relevant Self Organizing Maps (CRSOM), where the CRSOM method gives higher accuracy results compared to Backpropagation and Deep Learning. Context Relevant Self Organizing Maps (CRSOM) is chosen as a supervised learning classification algorithm that has an optimal internal representation, where data belonging different classes are separated with wider margin, while data belonging to the same class are clustered closely to each other. Thus, CRSOM is able to visualize high-dimensional protein data into binding site and non-binding site classes significantly. The results of the study obtained an average training accuracy of 99,60%, testing accuracy of 96.26%, and the average test time of 28.63 seconds, the result is better than the predecessor.

show abstract

Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers

Chattopadhyay

Iwema

Epstein

et al. 2019

Briefings in Bioinformatics

View full text Add to dashboard Cite

Biomedical researchers are increasingly reliant on obtaining bioinformatics training in order to conduct their research. Here we present a model that academic institutions may follow to provide such training for their researchers, based on the Molecular Biology Information Service (MBIS) of the Health Sciences Library System, University of Pittsburgh (Pitt). The MBIS runs a four-facet service with the following goals: (1) identify, procure and implement commercially licensed bioinformatics software, (2) teach hands-on workshops using bioinformatics tools to solve research questions, (3) provide in-person and email consultations on software/databases and (4) maintain a web portal providing overall guidance on the access and use of bioinformatics resources and MBIS-created webtools. This paper describes these facets of MBIS activities from 2006 to 2018, including outcomes from a survey measuring attitudes of Pitt researchers about MBIS service and performance.

show abstract

Developing a Bioinformatics Program and Supporting Infrastructure in a Biomedical Library

Cited by 6 publications

References 4 publications

Peer Teaching as Bioinformatics Training Strategy: Incentives, Challenges, and Benefits

Peer Teaching as Bioinformatics Training Strategy: Incentives, Challenges, and Benefits

Predicting Protein-Ligand Binding Site for Drug Design Using Context Relevant Self Organizing Maps (CRSOM)

Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers

Contact Info

Product

Resources

About