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Galaxy NUBRI Announcement
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Galaxy NUBRI: Democratizing Bioinformatics in Sudan

Galaxy NUBRI: Democratizing Bioinformatics in Sudan In Silico

Galaxy NUBRI: Democratizing Bioinformatics in Sudan

Overview

Galaxy NUBRI is a locally hosted, user-friendly bioinformatics platform established by the National University Biomedical Research Institute (NUBRI) to empower researchers, students, and healthcare professionals with accessible computational tools for genomic and biomedical data analysis. Built on the open-source.
Galaxy NUBRI enables users with minimal programming experience to perform complex bioinformatics analyses via a simple web interface. The platform supports a wide range of applications, including next-generation sequencing (NGS) workflows, variant calling, RNA-Seq analysis, metagenomics, epitope prediction, and more.

Objectives

  • To install and deploy a local Galaxy instance at NUBRI with essential bioinformatics tools and workflows.
  • To support genomic research, diagnostics, and drug discovery through an intuitive platform accessible to wet-lab scientists and clinicians.
  • To train staff, students, and external collaborators in the use of Galaxy for NGS data analysis, AMR surveillance, cancer genomics, and more.
  • To establish long-term collaboration with the African Galaxy Project and enable remote job execution and tool sharing with regional partners.
  • To ensure sustainability by building local technical capacity in server management, tool integration, and pipeline development.
Lead Investigator: Dr. Sofia Bashir Mohamed Ali
Funding Agency:
  • National University – Sudan

Research Phases

Phase One: Local Deployment of the Galaxy Platform

The steps successfully completed in Phase One included:

  • The server environment was configured using a Linux-based infrastructure, with all necessary dependencies and core Galaxy tools fully integrated.
  • A dedicated local web interface was established, enabling researchers at NUBRI and affiliated institutions to access bioinformatics workflows and pipelines related to genomics, transcriptomics, and molecular diagnostics.
  • Quality control of sequencing data (e.g., FastQC, Trimmomatic)
  • Genome assembly and annotation
  • Variant calling and alignment (e.g., BWA, GATK)
  • Gene expression analysis and visualization
  • Custom workflows for antimicrobial resistance and cancer genomics
Phase Two: Regional Integration with African Galaxy Network (Suspended)

The second phase aimed to integrate the local NUBRI Galaxy server with the African Galaxy Platform, a federated bioinformatics initiative coordinated by SANBI.

  • Enable cross-border data sharing and workflow harmonization among African research institutions
  • Provide access to cloud-based high-performance computing (HPC) resources
  • Facilitate collaborative training programs and tool development through regional partnerships
Future Plans

Upcoming developments to enhance Galaxy NUBRI functionality and collaboration:

  • Upgrade the Galaxy server with new tools for multi-omics integration and machine learning applications
  • Resume collaboration with SANBI for platform federation and remote job execution
  • Offer structured Galaxy training workshops for students and researchers in Sudan and the broader region
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What Our Alumni Say

Hear from our graduates who are making a difference in research and beyond

"I Was Master’s student in Bioinformatics at NUBRI, and the experience was truly inspiring.I chose NUBRI for its vision of connecting biology with technology and shaping the future of scientific research. Throughout the program and its workshops, I gained valuable knowledge, practical skills, and the confidence to grow as researchers. I remain deeply grateful to NUBRI for its support and for providing such a rich and motivating learning environment."

Aisha Khidir

Aisha Khidir

MSc Graduate – Bioinformatics

Batch 1

"My academic and professional development has been profoundly enriched through my engagement with the National University Bioinformatics Research Institute (NUBRI). The institute provided an exceptional platform for the advancement of my expertise in bioinformatics, computational biology, and biomedical data analysis. During my tenure at NUBRI, I undertook specialized training and completed several certification programs that significantly strengthened my research, analytical, and computational skills. The institute’s multidisciplinary environment, combined with the mentorship of highly qualified researchers, played a pivotal role in shaping my scientific perspective and fostering my professional growth. I am honored to be associated with NUBRI and to have contributed to its ongoing mission of promoting excellence in bioinformatics and life sciences research in Sudan and beyond."

Hla Faisal Abdalla

Hla Faisal Abdalla

MSc Graduate – Bioinformatics

Batch 1

"At first, I didn’t know anything about bioinformatics. By chance, I heard about the MSc in Bioscience at the National University (Medicine School), and we became the first batch. It turned out to be a great opportunity for me. I learned how to map, analyse, and handle genome sequencing to identify the causes of diseases—bacteria, viruses 🦠—especially those related to my field of dentistry. I gained practical laboratory experience 🧪🧫, learning how to handle and extract DNA. We were also visited multiple times by renowned lecturers from South Africa, who showed us how fast the field of bioinformatics is growing and how reliable it is for applications such as coronavirus outbreak analysis and vaccine development. Today, I have my name on three published papers in different medical fields—something I never imagined I could achieve. My sincere thanks 🙏 to the National University and the Institute of Bioscience for this opportunity"

Abdelmagid

Abdelmagid

MSc Graduate – Bioinformatics

Batch 1

"Being at the top of my Master’s in Bioinformatics class was a truly transformative experience. The program not only strengthened my scientific and computational skills, but also gave me the confidence to contribute to real-world biomedical research. Despite the challenges of the pandemic and the ongoing conflict, the institute’s dedication and support made a lasting impact on my academic growth and career path."

Abubakr A.

Abubakr A.

MSc Graduate – Bioinformatics

Batch 2

"I am Imam Ali Al-Riyah, a former Master’s student in Bioinformatics at NUBRI, and the experience was truly inspiring. I chose NUBRI for its vision of connecting biology with technology and shaping the future of scientific research. Throughout the program and its workshops, I gained valuable knowledge, practical skills, and the confidence to grow as a researcher. I remain deeply grateful to NUBRI for its support and for providing such a rich and motivating learning environment."

Imam Ali

Imam Ali

MSc Graduate – Bioinformatics

Batch 2

"I am Mohamed Jaafar Mohamed, one of the graduates of the Master's program in Bioinformatics at the National University. My experience began about two years before the start of the master’s program, when the university organized the first Bioinformatics workshop using Galaxy in Sudan. The workshop was successful and inspiring in both concept and execution, attracting many participants. From that moment, the idea of bioinformatics started to grow in my mind. When the admission for the second cohort opened, I was among the first to register. After waiting for nearly a year, the study period began. Although we faced several challenges — including political unrest and revolutions that often led to the postponement of lectures due to circumstances beyond the administration’s control — the institute’s management handled these difficulties wisely. The courses were well-designed, the professors were highly qualified, and a fully equipped laboratory with modern devices was made available to students. Despite all challenges, we successfully completed the study period. Then came the stage of research publication, which became even more difficult after the outbreak of war in Sudan. However, thanks to the continuous efforts and communication between the supervisors, administrative staff, and students — each in their respective locations — we were able to complete this wonderful journey. Despite the harsh conditions, the academic and scientific benefits we gained were invaluable. The program opened many doors for us in the professional field and enhanced our competitiveness even beyond Sudan"

Mohamed Gaafar

Mohamed Gaafar

MSc Graduate – Bioinformatics

Batch 2

"As a proud member of NUBRI, pursuing my Master’s degree in Bioinformatics has been a truly transformative journey. The program has broadened my knowledge and deepened my passion for the field. Despite the many challenges, the support from my colleagues kept me motivated, and I am deeply grateful to the institute’s administration whose constant encouragement gave me hope to keep moving forward. I’m proud and thankful to be part of such an inspiring institute."

Aya Elrasheed

Aya Elrasheed

MSc Graduate – Bioinformatics

Batch 3

"My academic journey at NUBRI has been an invaluable opportunity to acquire profound knowledge that has become a cornerstone for both my professional and academic paths. During this time, I had the privilege of meeting an exceptional group of experts and specialists. Each individual represented a unique realm of expertise, embodying a rich diversity of knowledge and a commitment to delivering advanced educational content—a credit to the institute's management. Thanks to this experience, I am now better equipped to grasp the immense potential created by integrating life sciences with computer science and understanding its vast horizons. Despite the challenges and difficulties we faced during the conflict in Sudan, the institute remained steadfast in its educational mission, exerting every effort to overcome obstacles and continue the educational journey. NUBRI is, without a doubt, that unique place where qualified minds converge to shape generations of distinguished innovators and researchers."

Khalid Berma

Khalid Berma

MSc Graduate – Bioinformatics

Batch 3

"My Experience at the Institute of Bioinformatics I hold a PhD in the medical field, and completing my Master’s degree at the Institute of Bioinformatics was a transformative milestone in my academic journey. The program significantly enhanced my knowledge and research capabilities, allowing me to gain deeper insights into modern bioinformatics tools and their applications in medical research. I truly believe that every researcher with a PhD in the medical field would benefit greatly from pursuing a Master’s in Bioinformatics, as it broadens scientific understanding, sharpens analytical and research skills, and opens up new interdisciplinary research opportunities. My experience at the Institute was exceptional — the academic environment was inspiring, and the faculty and staff were highly professional, supportive, and respectful throughout my studies."

Qutoof Hashim

Qutoof Hashim

MSc Graduate – Bioinformatics

Batch 3

"During my time with NUBRI as an attached research assistant, I had the privilege of contributing to in silico vaccine design, an experience that transformed my understanding of bioinformatics. What began as an unfamiliar field soon became a deep passion, fueled by the supportive and intellectually stimulating environment that NUBRI offered. Under the exceptional mentorship of Dr. Sofia, I learned from one of the best minds in the field-gaining not only technical skills but also the mindset of innovation and scientific curiosity. Working alongside some of the most driven, creative, and committed colleagues, I found a community that shared my motivation and constantly pushed me to excel. NUBRI became more than a research zone; it was a space where ambition met collaboration, where ideas turned into breakthroughs, and where I discovered the joy of scientific exploration and creative problem-solving"

Ahmed Abdelghyoum

Ahmed Abdelghyoum

Research Attachment Program

"Working with the National University Biomedical Research Institute has been a valuable professional experience. I assisted in online H3BioNet Courses, I contributed to student learning while strengthening my own academic skills. I gained hands-on experience in using bioinformatics software to perform proteome filtration in a project that resulted in a published paper. This experience enhanced my skills in computational biology and deepened my understanding of how bioinformatics supports biomedical discoveries. I appreciate the laboratory’s supportive environment, high scientific standards, and commitment to excellence in research."

Samah Omar

Samah Omar

Research Attachment Program

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