scholarly journals Community development, implementation, and assessment of a NIBLSE bioinformatics sequence similarity learning resource

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257404
Author(s):  
Adam J. Kleinschmit ◽  
Elizabeth F. Ryder ◽  
Jacob L. Kerby ◽  
Barbara Murdoch ◽  
Sam Donovan ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Sequence Similarity ◽  
Student Assessment ◽  
Similarity Learning ◽  
Biological Sequence ◽  
Assessment Data ◽  
Learning Materials ◽  
Learning Resource ◽  
Science Courses ◽  
Educational Product

As powerful computational tools and ‘big data’ transform the biological sciences, bioinformatics training is becoming necessary to prepare the next generation of life scientists. Furthermore, because the tools and resources employed in bioinformatics are constantly evolving, bioinformatics learning materials must be continuously improved. In addition, these learning materials need to move beyond today’s typical step-by-step guides to promote deeper conceptual understanding by students. One of the goals of the Network for Integrating Bioinformatics into Life Sciences Education (NIBSLE) is to create, curate, disseminate, and assess appropriate open-access bioinformatics learning resources. Here we describe the evolution, integration, and assessment of a learning resource that explores essential concepts of biological sequence similarity. Pre/post student assessment data from diverse life science courses show significant learning gains. These results indicate that the learning resource is a beneficial educational product for the integration of bioinformatics across curricula.

scholarly journals Designing and developing an app to perform Hofstee cut-off calculations

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 450
Author(s):  
Ken Masters ◽  
Nadia Al-Wardy
Keyword(s):  
Medical Education ◽  
Student Assessment ◽  
Education Student ◽  
Assessment Data ◽  
Traditional Methods ◽  
Android App

Determining a Hofstee cut-off point in medical education student assessment is problematic: traditional methods can be time-consuming, inaccurate, and inflexible.  To counter this, we developed a simple Android app that receives raw, unsorted student assessment data in .csv format, allows for multiple judges’ inputs, mean or median inputs, calculates the Hofstee cut-off mathematically, and outputs the results with other guiding information. The app contains a detailed description of its functionality.

A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases

2010 ◽  
Vol 2 (4) ◽  
pp. 1-11
Author(s):  
Dan Wei ◽  
Qingshan Jiang ◽  
Sheng Li
Keyword(s):  
Nucleic Acid ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Biological Sequence ◽  
Nucleic Acid Bases ◽  
New Approach ◽  
Characteristic Distribution ◽  
Sequence Similarity Analysis

Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of length L, reflects the valuable information contained in a biological sequence and thus may be used in DNA sequence similarity analysis. However, similarity analysis based on characteristic distribution of L-tuple is not effective for the comparison of highly conservative sequences. In this paper, a new similarity measurement approach based on Triplets of Nucleic Acid Bases (TNAB) is introduced for DNA sequence similarity analysis. The new approach characterizes both the content feature and position feature of a DNA sequence using the frequency and position of occurrence of TNAB in the sequence. The experimental results show that the approach based on TNAB is effective for analysing DNA sequence similarity.

Teaching Educators How to Use Student Assessment Data to Improve Instruction

2005 ◽  
Vol 86 (9) ◽  
pp. 700-706 ◽  
Author(s):  
Kathryn Parker Boudett ◽  
Richard J. Murnane ◽  
Elizabeth City ◽  
Liane Moody
Keyword(s):  
Student Assessment ◽  
Assessment Data ◽  
Improve Instruction

scholarly journals An Evaluation of Department of Education Produced Grade 7 Biology Modules by Biology Experts and Science Teachers

2019 ◽  
Vol 27 (5) ◽  
Author(s):  
Maria Lourdes G. Tan
Keyword(s):  
Biological Sciences ◽  
Science Teachers ◽  
Doctoral Degree ◽  
Bachelor's Degree ◽  
Department Of Education ◽  
Survey Method ◽  
Learning Materials ◽  
Teaching Learning ◽  
Evaluation Of Learning ◽  
Descriptive Survey

Teachers play an essential role in the evaluation of learning materials. As facilitators of learning, they ensure that learning materials serve their purpose of bringing about the effective teaching-learning process. This study aimed to evaluate the Department of Education (DepEd)-produced Grade 7 Biology Modules as perceived by Biology Experts and Science Teachers in the 16 public secondary schools in the Division of Tacloban City, Leyte, Philippines. The modules are evaluated based on the seven dimensions: a) content, b) presentation and organization, c) learning activities, d) evaluation activities, e) accuracy and up-to-dateness of information, f) format and g) sufficient availability of materials. The demographic profile of 17 Biology experts showed that the majority are female, BSED graduates in Biological Sciences with a doctoral degree in Biology and 1-15 years teaching Biology subjects. Grade 7 Science teachers are mostly females who have a bachelor's degree in Biological Sciences, with master's units and 1-2 years teaching Grade 7 Science in the K to 12 Curriculum. Biology experts and science teachers assessed the five modules using descriptive survey method employing quantitative and qualitative analysis. They both evaluated the modules satisfactory in the seven dimensions. However, they pointed out suggestions for improvement of the modules. Keywords: Biology Experts, Teachers, Modules, Evaluation

scholarly journals Pengembangan perangkat pembelajaran pencemaran lingkungan berbasis inkuiri terbimbing melalui pemanfaatan potensi wilayah industri mojokerto sebagai sumber belajar untuk mengembangkan pemahaman konsep, keterampilan ilmiah, dan sikap ilmiah siswa kelas VII SMPN 2 Sooko

2021 ◽  
Vol 1 (3) ◽  
pp. 163-172
Author(s):  
Indrias Ma’rufinia ◽  
Ibrohim Ibrohim ◽  
Vita Ria Mustikasari
Keyword(s):  
Learning Material ◽  
Guided Inquiry ◽  
Evaluation Instrument ◽  
Scientific Attitude ◽  
Learning Materials ◽  
Learning Resource ◽  
Test Result

The purpose of this research was to produce a learning instrument based on guided inquiry by the usage of potency area as learning resource were valid and reasonable to be used. The research used Borg and Gall’s developing model. The result of this research is the learning materials were included of syllabus, learning implementation design, student worksheet, handout, and evaluation instrument showed the learning materials valid with that validity was 96.9 percent. The test result of implementation of learning material showed got very practical criteria in 91,9 percent value. The test result of learning material showed that the student concept comprehension was 82,6 with high criteria, scientific skill was 88,3 with high criteria, and scientific attitude was 91,0 with high criteria. The result research showed that learning materials reasonable to be used. Tujuan penelitian ini untuk menghasilkan produk perangkat pembelajaran berbasis inkuiri terbimbing melalui pemanfaatan potensi wilayah sebagai sumber belajar yang valid dan layak digunakan. Penelitian ini menggunakan model pengembangan Borg and Gall (1983). Hasil dari penelitian ini adalah perangkat pembelajaran yang berupa silabus, RPP, LKS, handout dan instrumen penilaian yang valid dengan nilai validitas sebesar 96,9 persen. Hasil uji keterlaksanaan perangkat pembelajaran menunjukkan nilai sebesar 91,9 persen dengan kriteria sangat praktis. Hasil uji coba perangkat pembelajaran menunjukkan bahwa nilai rata-rata pemahaman konsep sebesar 82,6 dengan kriteria tinggi, nilai keterampilan ilmiah sebesar 88,3 dengan kriteria tinggi, dan nilai sikap ilmiah sebesar 91,0 dengan kriteria tinggi. Berdasarkan hasil yang diperoleh menunjukkan perangkat pembelajaran layak digunakan.

scholarly journals EnTrance: Exploration of Entropy Scaling Ball Cover Search in Protein Sequences

2021 ◽  
Author(s):  
Yoonjin Kim ◽  
Zhen Guo ◽  
Jeffrey A. Robertson ◽  
Benjamin Reidys ◽  
Ziyan Zhang ◽  
...  
Keyword(s):  
Search Algorithm ◽  
Sequence Similarity ◽  
Protein Sequences ◽  
Biological Data ◽  
Biological Databases ◽  
Biological Sequence ◽  
Absolute Size ◽  
Sequence Identification ◽  
Build Time ◽  
Search Approach

Biological sequence alignment using computational power has received increasing attention as technology develops. It is important to predict if a novel DNA sequence is potentially dangerous by determining its taxonomic identity and functional characteristics through sequence identification. This task can be facilitated by the rapidly increasing amounts of biological data in DNA and protein databases thanks to the corresponding increase in computational and storage costs. Unfortunately, the growth in biological databases has caused difficulty in exploiting this information. EnTrance presents an approach that can expedite the analysis of this large database by employing entropy scaling. This allows scaling with the amount of entropy in the database instead of scaling with the absolute size of the database. Since DNA and protein sequences are biologically meaningful, the space of biological sequences demonstrates the structure exploited by entropy scaling. As biological sequence databases grow, taking advantage of this structure can be extremely beneficial for reducing query times. EnTrance, the entropy scaling search algorithm introduced here, accelerates the biological sequence search exemplified by tools such as BLAST. EnTrance does this by utilizing a two step search approach. In this fashion, EnTrance quickly reduces the number of potential matches before more exhaustively searching the remaining sequences. Tests of EnTrance show that this approach can lead to improved query times. However, constructing the required entropy scaling indices beforehand can be challenging. To improve performance, EnTrance investigates several ideas for accelerating index build time that supports entropy scaling searches. In particular, EnTrance makes full use of the concurrency features of Go language greatly reducing the index build time. Our results identify key tradeoffs and demonstrate that there is potential in using these techniques for sequence similarity searches. Finally, EnTrance returns more matches and higher percentage identity matches when compared with existing tools.

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