Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Developing digital competence of teachers in postgraduate education using Google Workspace for Education

Digital competence is a key skill for teachers in the era of distance education. However, developing digital competence requires appropriate forms and training methods that utilise the available technologies and tools. In this article, we explore how Google Workspace for Education, a cloud service that offers various digital education tools, can foster digital competence among teachers in postgraduate education. We draw on our experience organising and conducting distance learning courses for university teachers at the Department of Open Educational Systems and Information and Communication Technologies of the Institute of Postgraduate Education. We present the theoretical background of competence, digital competence, and distance education and the educational opportunities that Google Workspace for Education provides. Using Google Classroom as the main platform, we describe the effective ways of developing digital competence in distance learning. We analyse the participants' learning outcomes and the benefits of collaborative learning. We also report the results of our research on developing teachers' digital competence based on selected criteria and indicators. We highlight the promising trends and challenges in developing teachers' digital competence in distance education

A roadmap for the functional annotation of protein families: a community perspective.

Funder: U.S. National Library of MedicineOver the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward