Dear CSI Researchers,​

We are excited to bring you the April edition of our monthly newsletter dedicated to keeping the CSI research community updated on the latest in bioinformatics and computational biology.

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CSI x AWS Office Hours 🤝​

We’re in the process of organizing an office hours collaboration between CSI Labs and AWS. As our needs for storage and compute resources continue to grow, it’s the perfect time to engage with one of the world’s leading cloud providers for expert guidance and insights.

To help us shape these sessions effectively, we’d appreciate your input. Your feedback will be instrumental in tailoring the agenda for this collaboration.

Survey Link

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New Tools and Software Updates 🧰​

Dorado Update 🚀​

Oxford Nanopore's basecalling software has received a recent update, bringing speed improvements to high accuracy (HAC) and super accurate (SUP) basecalling models. For those of you interested in genome assembly, you will also enjoy speed improvements for read denoising and assembly. The update also offers accuracy improvements for polyA-tail estimation.

• More information: Available on GitHub

SG-Nex long-read data release 🧬​

Long-read data and analysis from the Singapore Nanopore Expression Project (SG-Nex) was recently published. The repository includes data sequenced from seven human cell lines using three different library prep methods (dRNA, dcDNA, and cDNA). The raw and processed data from the study are publicly available online and free to download.

• Data Release: Available on AWS
• Data access tutorial: Learn more on GitHub
• Research details: Manuscript available in Nature Methods

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GeDaC Resource updates​

Facility Website Updates​

We're pleased to announce that we've updated our GeDaC website with improved navigation, new resource pages, and enhanced documentation. These changes make it easier for you to find the information and tools you need for your research.

CloudFlow Platform​

Our CloudFlow platform continues to provide CSI researchers with access to best-practice bioinformatics pipelines in the cloud. Remember that our team is available to assist with your computational needs and pipeline implementations.

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Best regards,
GeDaC Team, CSI - NUS
📧 support@gedac.org
🌐 Website | 🔗 GitHub | 🛠️ Helpdesk

Dear CSI Researchers,​

We are excited to bring you the second edition of our monthly newsletter dedicated to keeping the CSI research community updated on the latest in bioinformatics and computational biology.

This month, we're highlighting some exciting new tools and an upcoming workshop opportunity that may benefit your research endeavors.

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New Tools and Software Updates 🧰​

Dorado Update 🚀​

Oxford Nanopore's basecalling software has received a significant update that brings impressive speed improvements for Nvidia GPUs, particularly Ampere-based GPUs. This enhancement will accelerate nanopore sequencing data processing workflows.

• More information: Available on GitHub

Realfreq Tool Release 🧬​

A new tool for calling methylated bases from MinION and PromethION flow cells has been released. What makes Realfreq particularly valuable is its ability to call methylated bases in real-time while the sequencing instrument is running.

• Availability: Completely open source on GitHub
• Research details: Preprint available on bioRxiv

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Upcoming Conferences and Workshops 🗓️​

AWS Genomics Workshop at NUS​

Amazon Web Services (AWS) is hosting a genomics workshop to help NUS researchers explore cloud computing applications in genomics research. This in-person event provides a great opportunity for students and staff to meet with AWS leadership and learn more about alternative computing and storage resources.

• 📅 Date: March 18, 2025
• 📍 Location: MD6-03-01S
• 🔗 Apply here

Singapore Long-Read Symposium – Dr. Heng Li's Talk​

The Singapore Long-Read Symposium has invited Dr. Heng Li (Dana-Farber Cancer Institute), a pioneer in bioinformatics, to give a presentation. Dr. Li has developed many widely used genomics tools and file formats, making a profound impact on the field. Don't miss this chance to hear from a leading expert!

• 📅 Date: March 13, 2025
• 🎤 Speaker: Dr. Heng Li
• 🔗 Register now to reserve your seat!

CSHL Chromatin, Epigenetics and Gene Expression Course​

Cold Spring Harbor Laboratory (CSHL) is offering a specialized course for students, postdocs, and principal investigators in New York, USA. This is an excellent opportunity to:

• Gain grant writing experience

• Network with international scientists

• Learn cutting-edge technologies applicable to your research

• 💰 Financial Support: Stipends available for international applicants

• 📅 Application Deadline: March 31st, 2025

• 🔗 How to apply: Apply here

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GeDaC Resource updates​

Facility Website Updates​

We're pleased to announce that we've updated our GeDaC website with improved navigation, new resource pages, and enhanced documentation. These changes make it easier for you to find the information and tools you need for your research.

CloudFlow Platform​

Our CloudFlow platform continues to provide CSI researchers with access to best-practice bioinformatics pipelines in the cloud. Remember that our team is available to assist with your computational needs and pipeline implementations.

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Best regards,
GeDaC Team, CSI - NUS
📧 support@gedac.org
🌐 Website | 🔗 GitHub | 🛠️ Helpdesk

Dear CSI Researchers,​

We are happy to announce a monthly newsletter dedicated to keeping you informed about the latest updates in bioinformatics and computational biology research at CSI.

Our goal is to provide faculty, students and staff with updates on recent research, new tools, career opportunities, and information about events, conferences, workshops and internships - that can benefit staff and students involved in genomics research.

We also plan to highlight and provide updates on resources available to researchers via the Genomics and Data Analytics Core (GeDaC) at CSI.

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Featured Resource: CloudFlow 🚀​

CloudFlow 🚀, is a web-based platform designed specifically for computational biology research at CSI. It provides:

• Easy access to best-practice bioinformatics pipelines running in the cloud
• Current focus on RNA-related pipelines
• Opportunities for expansion based on researcher needs

For more information about the platform, please visit our documentation.

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What to Expect Each Month​

• 📊 Summaries of recent bioinformatics research
• 🧬 Announcements of new tools, software and data releases
• 🗓️ Upcoming conferences, workshops and internships
• 📈 Resource updates from the GeDaC team

We are thrilled to equip you and your teams with the latest information and resources to stay ahead in this rapidly evolving field and propel your research forward.

Connect With Us​

If you have any news, research, or announcements for the newsletter, or if you have questions, feedback, or need support, we'd love to hear from you!

Feel free to reach out at support@gedac.org, and we'll get back to you as soon as possible.

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Best regards,
GeDaC Team, CSI - NUS
📧 support@gedac.org
🌐 Website | 🔗 GitHub | 🛠️ Helpdesk