Evaluation of the Effectiveness of the Genomics & Science DOJO 3.0 Learning Method in Improving Research Skills and Scientific Writing Among Researchers in Indonesia

Evaluation of the Effectiveness of the Genomics & Science DOJO 3.0 Learning Method in Improving Research Skills and Scientific Writing Among Researchers in Indonesia: A Randomized Controlled Trial

The goal of this study is to rigorously evaluate the effectiveness of the DOJO 3.0 learning methodology in enhancing research skills and scientific writing among researchers in Indonesia compared to non-DOJO learning method. The main questions it aims to answer are:

How effective is the Dojo 3.0 methodology in improving participants' research skills and scientific writing, including critical thinking, data analysis ability, knowledge acquisition, and scientific manuscript quality and publication progress? How do participants' experiences, perceptions of the learning process and teaching quality, as well as their engagement, performance, and learning behaviors, differ between the intervention (DOJO) and control groups throughout the program?

Researchers will compare two groups, control group and intervention group to see if there is a significant difference between these two groups.

Standard learning method Non-DOJO (Control) DOJO learning method (Intervention)

For the intervention group, participants will participate in Shinjitsu class, an interactive dynamic lecture with real time engagement, an offline minicamp session with lecture that is more intense, intentionally more provocative and dynamic, wounded healer, shinjitsu ninja obstacles, shinjitsu ninja run, sparring and Tournament.

Study Overview

• Status: Not yet recruiting
• Conditions: Genomics; Workshop; Critical Thinking Skill; Data Analysis Skill; Personal Empowerment; Manuscript Quality; Science; Research Publication; Learning Methodology; Quality of Teaching
• Intervention / Treatment: Behavioral: Standard Learning Methodology; Behavioral: Genomics & Science Dojo Learning Methodology

Detailed Description

Detailed Description

This study is using a randomised controlled trial method conducted in Jakarta, Indonesia, designed to rigorously evaluate the effectiveness of the DOJO 3.0 learning methodology in enhancing research skills and scientific writing among researchers in Indonesia compared to non-DOJO learning methods.

This study consists of a cluster randomized trial with two intervention arms, to evaluate the effectiveness of the genomics and science DOJO 3.0 learning method, specifically comparing between standard learning method and DOJO learning method. The DOJO learning method will be delivered through structured components, including modularized minicamps, structured mentoring, expanded Shinjitsu tournaments, and the introduction of the Shinjitsu Ninja component, providing a platform for scientific capacity building, collaboration, and innovation.

To support implementation across both study components, several structured operational procedures will be applied. To minimize contamination between groups,activities for the control and intervention arms will be conducted in separate locations. However, to ensure consistency in content delivery, both groups will receive the same core instructional materials and be taught by the same instructors (Sensei). The primary distinction between groups will lie in the learning approach and environment, with the intervention group receiving the DOJO learning method and the control group receiving a standard (non-DOJO) learning method.

• Sample Size and Statistical Considerations The sample size calculation is based on the expected effect size of the intervention on primary outcomes (critical thinking, knowledge improvement, data analysis, personal empowerment, manuscript quality and quality of teaching), anticipated attrition among participants, and statistical power considerations to ensure meaningful results. Taking these factors into account, it is estimated that approximately 48 teams or 96 individuals will be recruited and participating in this study.
• Quality Assurance and Data Management A comprehensive quality assurance framework will be implemented to ensure data integrity, accuracy, and consistency across all study sites. Electronic data capture systems will incorporate built-in validation rules, including range checks, consistency checks, and logical constraints across related variables.

Routine centralized data monitoring will be conducted to assess data completeness, timeliness, and internal consistency. Key indicators will include baseline/endline test results, activity logs, pre- and post-test results, and other study-related outputs, which will be systematically reviewed and used as primary inputs for analysis.

A standardized data management system will be implemented, including a comprehensive data dictionary that defines all study variables, formats, permissible values, coding structures, and data sources. Where applicable, standardized coding approaches will be applied to ensure consistency.

All study procedures will be guided by Standard Operating Procedures (SOPs) and a detailed manual to ensure standardized implementation across sites.

• Handling of Missing Data Data quality checks during data collection will aim to minimize missingness. During analysis, appropriate statistical techniques, such as multiple imputation will be applied as specified in the statistical analysis plan. In cases where key supporting variables, such as participants' educational background and research stage, are missing, efforts will be made to retrieve this information from participants or relevant records.
• Statistical Analysis Plan All analyses will follow the intention-to-treat principle. Primary analyses will assess effectiveness of the DOJO learning method across intervention arms using quantitative methods to account for cluster randomization and potential confounders.

Primary analysis will examine differences in participants' critical thinking, improvement of knowledge, data analysis skills, personal empowerment, manuscript quality, publication, and quality of teaching. These outcomes will be assessed using structured assessment scoring and appropriate statistical models, by comparing endline results with baseline measurement.

Secondary analysis will assess differences in activity effectiveness, such as lecture and activity (i.e Ninja obstacles), or lectures only. These outcomes will be assessed using a structured assessment scoring and appropriate statistical models, by comparing post-test results with pre-test results that are administered each day of the minicamp offline session.

Depending on the nature of the outcome variables, appropriate statistical models will be applied. Continuous outcome variables like daily pre and post test scores, knowledge improvements, critical thinking scores, journal scores, tournament or mini tournament scores, and days distance to submission, will be primarily analyzed with repeated ANCOVA which is implemented to assess the changes over the time for each observation within the teams. Binary outcomes, such as paper finished or workshop completion, will be analyzed with chi-square test or logistic regression. Beside being analyzed as a variable, days distance to publication that act as a time-related outcomes, may be explored using survival analysis.

All analysis will include baseline characteristics of the participants, including the stratification of the research stage when joining the program and educational background, to improve comparability and reduce confounding.

• Study Type: Interventional
• Enrollment (Estimated): 96
• Phase: Not Applicable

Contacts and Locations

• Study Contact: Name: Lia Rosida; Phone Number: +6287765680206; Email: lia.rosida@sid-indonesia.org

Study Locations

• Indonesia
  • West Nusa Tenggara
    • Mataram, West Nusa Tenggara, Indonesia, 83238
      • Summit Institute for Development

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: Yes

Description

Inclusion Criteria:

• Registered participants of Genomics & Science DOJO 3.0
• Teams consisting of two members
• Submission of research concept note
• Completion of screening and assessment stages (administratively and substantially through blind concept note screening and team's curriculum vitae)
• Willingness and commitment to participate in the full program will be ensured through a structured confirmation process.
• In addition, participants will be required to review, sign, and submit a commitment letter outlining the full schedule, expectations for attendance, and participation requirements.
• Information regarding program schedule and participation expectations will be communicated at multiple stages, including during registration, program launch, and post-selection, to ensure participants are fully informed prior to confirming their participation.
• Involvement/ attendance of the first author

Exclusion Criteria:

• Incomplete registration or documentation
• Failure to meet team composition requirements
• Withdrawal before intervention
• Incomplete baseline data

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Other
• Allocation: Randomized
• Interventional Model: Parallel Assignment
• Masking: Double

Number of Arms

2

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Active Comparator: Standard Learning Method; Participants receive: Standard learning method Regular teaching style and digital material	Behavioral: Standard Learning Methodology; A structured standard learning approach that is conceptually adapted from the teaching and learning methods used in the MSc in Health Service Improvement and Evaluation (HSIE) at the University of Oxford. In the Shinjitsu class, the material will be delivered in a fully didactic, one-way format, limiting participant interaction to brief, moderator-led question-and-answer sessions. The Wounded Healer session will be conducted as a seminar focused on individual reflection rather than interactive sharing, resulting in a more passive reflective experience without the experiential and positive psychology components present in the DOJO intervention. For Ninja Run, participants will not be placed in a competitive environment but will instead be given time to complete tasks at their own pace without time pressure, thereby not experiencing the same level of cognitive demand as working under constraints.
Experimental: Genomics & Science Learning Methodology; Participants receive: DOJO 3.0 Learning Method Regular teaching style and digital material	Behavioral: Genomics & Science Dojo Learning Methodology; The key characteristic of the DOJO approach lies in the Shinjitsu methodology, which integrates structured debate, confrontational argumentation, and real-time intellectual challenge as core mechanisms to stimulate critical thinking. The program will be implemented through structured components by continuing several activities such as Wounded Healer, Ninja Run, and Shinjitsu Tournament. Wounded Healer is based on the principles of active psychology and leverages direct and interactive experiences. In this session, participants actively share challenges encountered in a supportive environment, thereby fostering confidence and psychological safety. This is followed by Ninja Run, where participants train their critical thinking and decision-making skills under constrained conditions. Participants engage in a structured Shinjitsu Tournament, in which they not only present their arguments but also defend and critically challenge them in a confrontational yet structured setting.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Personal Empowerment	Personal empowerment will be assessed based on participants' confidence and sense of agency in engaging with and completing program-related tasks. Raw scores from the Dojo-specific validated questionnaire will be calculated separately at pre- and post-assessment. Pre-to-post changes will be standardized (z-scores) to enable comparability across instruments with different scoring scales. Standardized scores from both measures will then be equally weighted and combined to generate a composite Personal Empowerment Index. Changes in the Personal Empowerment Index are compared between control and intervention groups to assess program impact.	Baseline and one month
Critical Thinking	Critical thinking abilities will be measured using open-ended questions. measured quantitatively using the Holistic Critical Thinking Scoring Rubric (HCTSR). The primary metric is the mean change score between intervention and control groups, estimated using analysis of covariance (ANCOVA) with baseline MCQ scores as covariate. Critical thinking is assessed using a 5-item questionnaire, which will be scored by trained reviewers on a 1-4 rubric (1: Significantly weak, 2: Unacceptable, 3: Acceptable, 4: Strong), with 0 indicating no responses or no demonstration of critical thinking. Total score ranges from 0 to 20. Higher scores indicate better critical thinking performance.	Baseline and one month
Knowledge Improvement	Improvement of knowledge will be measured using multiple-choice questions (MCQs) through three sessions from each different program contents: Day 1(30 items, score range 0-30), Day 2 (40 items, score range 0-40), and Day 3 (30 items, score range 0-30). One point is awarded for each session per correct answer. A higher score means better knowledge. Scores will be calculated as the percentage of correct answers (%) for each team participant. The primary metric is the adjusted mean difference in endline MCQ scores between intervention and control groups, estimated using ANCOVA with baseline MCQ scores as covariate.	Baseline and one month
Data Analysis	Data analysis skills are assessed at the individual participant level through case-based written assessments administered before and after the intervention. The pre-test (Ninja Obstacles) is completed individually by each participant before program content is delivered, and the post-test (Ninja Run) is completed individually on the final day of the program. In both assessments, participants independently analyze a real-world health dataset and submit a written response covering data interpretation, calculation, and application. The rubric assesses the responses in four criteria: data interpretation, application of basic quantitative analysis, evidence-based conclusions, and communication of key findings. Each criterion is scored on a 5-point scale (1= lowest performance, 5= highest performance), with 0 indicating performance of data analysis. Criterion scores are summed to a total individual score ranging from 4 to 20, with higher scores illustrating better data analysis performance	Baseline and one month
Manuscript Quality	The improvement in manuscript quality submitted by the team participants, comparing before and after to DOJO activity. This variable will be measured using previous DOJO's evaluator scoring, specifically adapted from high-impact journal reviewer guidelines (BMJ, Nature, Elsevier, JAMA) and reporting guidelines (CONSORT, STROBE, PRISMA). The rubric covers four domains: Scientific Content and Rigor (35 points), Reporting Quality (20 points), Scientific Writing Quality (25 points), and Journal Readiness and Impact (20 points). Total scores range from 0 to 100, with higher scores indicating better manuscript quality. Each manuscript is scored by at least two blinded evaluators.	Baseline and one month

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Participants' Publication	This variable will be assessed based on efficiency and quality of participants' manuscript publications, including submission timelines, publication speed, and journal impact. Impact on publication outcomes will be measured using a composite scoring approach. The Submission-to-Publication Interval Score will be calculated based on the number of months between manuscript submission and publication, with shorter intervals receiving higher scores (≤3 months = 4; ≤5 months = 3; ≤7 months = 2; ≤9 months = 1; not published = 0). Journal quality will be assessed using quartile rankings, with scores assigned as follows: Q1 = 3, Q2 = 2, Q3 = 1, and Q4 or unindexed journals = 0.	Baseline and nine months
Quality of Teaching	This variable measures participants' perceptions of how effective the teaching was, both overall and at the Sensei level (clarity, structure, engagement, and learning support). Average scores (1-5 scales) are calculated for overall teaching quality and per Sensei (1: Strongly disagree, 2: Disagree, 3: Neutral, 4: Agree, 5: Strongly Agree). Then, it was aggregated for comparison between the intervention and control groups. Higher scores indicate better quality of teaching.	Baseline and one month

Collaborators and Investigators

• Sponsor: Summit Institute for Development, Indonesia
• Collaborators: Oxford University Clinical Research Unit Indonesia

Publications and helpful links

General Publications

• Chicco D, Sichenze A, Jurman G. A simple guide to the use of Student's t-test, Mann-Whitney U test, Chi-squared test, and Kruskal-Wallis test in biostatistics. BioData Min. 2025 Aug 20;18(1):56. doi: 10.1186/s13040-025-00465-6.
• Braga LH, Farrokhyar F, Donmez MI, Nelson CP, Haid B, Herbst K, Garriboli M, Cascio S, Nieuwhof-Leppink A, Kaefer M, Bagli DJ, Kalfa N, Ching C, Fossum M, Harper L. Randomized controlled trials - The what, when, how and why. J Pediatr Urol. 2025 Apr;21(2):397-404. doi: 10.1016/j.jpurol.2024.11.021. Epub 2024 Dec 3.
• Akobeng AK. Assessing the validity of clinical trials. J Pediatr Gastroenterol Nutr. 2008 Sep;47(3):277-82. doi: 10.1097/MPG.0b013e31816c749f.
• Widyahening IS, Wangge G, Saldi SR, Lestari BW, Apriani L, Sastroasmoro S, Glasziou P, van der Graaf Y, van der Heijden GJ. Quality and reporting of publications by Indonesian researchers: a literature survey. J Evid Based Med. 2014 Aug;7(3):163-71. doi: 10.1111/jebm.12112.

Study record dates

Study Major Dates

• Study Start (Estimated): May 20, 2026
• Primary Completion (Estimated): June 30, 2026
• Study Completion (Estimated): March 30, 2027

Study Registration Dates

• First Submitted: May 18, 2026
• First Submitted That Met QC Criteria: May 18, 2026
• First Posted (Actual): May 26, 2026

Study Record Updates

• Last Update Posted (Actual): May 28, 2026
• Last Update Submitted That Met QC Criteria: May 24, 2026
• Last Verified: May 1, 2026

More Information

Terms related to this study

• Keywords: Randomized Controlled Trial; Critical Thinking; Learning Method; Research Skill; Scientific Writing; Genomics and Science
• Additional Relevant MeSH Terms: Genetic Structures; Genetic Phenomena; Genome
• Other Study ID Numbers: 400422-412 (Other Grant/Funding Number: Foreign, Commonwealth and Development Office, British Embassy Jakarta)

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO
• IPD Plan Description: IPD will not be shared due to confidentiality obligations and restrictions under the participant consent agreement

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No