Navigating SAGE as a Beginner: Tips for Getting Started

In summary, the conversation discusses the use of SAGE, a mathematical software, and the speaker's experience with it. They mention being in a lockdown and wanting to explore SAGE, but feeling intimidated when trying to find resources online. They also ask for tips and mention previous experience with SAGE through a university lab. Another person shares their experience with SAGE in linear algebra and graph theory, suggesting some helpful books for beginners.
  • #1
karush
Gold Member
MHB
3,269
5
OK I am in a lock down here with my Governor ordering us stay hometho

So thot I would jump off the diving board into the world of SAGE

However when I went to google for guiding light on this I got intimidated fastSo Does anyone done square one and more I would like some tips

I did some SAGE about a year ago but it was a University Lab with a lot of help
I have forgotten everything...

thanks ahead...

I do know that SAGE is collaborative with Latex so that is a big plus
 
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  • #2
I've been using Sage for generating problems in linear algebra and graph theory. It has nice functions for generating random matrices with integer reduced row echelon form. But I am only a beginner. I am working with text command line.

There are a couple of books: Sage for Undergraduates, and Computational Mathematics with SageMath. They are easy to find online.
 

1. What is SAGE and how is it used in scientific research?

SAGE (Serial Analysis of Gene Expression) is a method used to analyze gene expression in biological samples. It involves sequencing small snippets of RNA, which can then be used to identify and quantify the expression of various genes in a sample. This information can be used to understand how genes are regulated and how they contribute to specific biological processes.

2. Why should I use SAGE in my research?

SAGE is a powerful and versatile tool for gene expression analysis. It allows for high-throughput sequencing of gene transcripts, providing a comprehensive view of gene expression in a sample. Additionally, SAGE does not rely on prior knowledge of gene sequences, making it useful for studying non-model organisms or identifying novel genes.

3. How do I get started with SAGE?

To get started with SAGE, you will first need to design your experiment and collect your biological samples. Then, you will need to extract and purify RNA from your samples. Next, you will perform the SAGE protocol, which involves converting the RNA into short snippets and sequencing them. Finally, you will analyze the sequencing data using specialized software or tools, such as SAGEmap or SAGE Genie.

4. What are some tips for navigating SAGE as a beginner?

Some tips for beginners using SAGE include thoroughly understanding the protocol before beginning, carefully planning your experiment and sample preparation to ensure accurate results, and using reliable and up-to-date software for data analysis. It is also important to consult with experienced researchers or seek out training or tutorials to ensure a successful SAGE experiment.

5. Are there any potential challenges or limitations to using SAGE?

While SAGE is a powerful tool, it does have some limitations. For example, it may not accurately detect low levels of gene expression or distinguish between alternative splicing events. Additionally, the cost and time required for SAGE may be prohibitive for some research projects. It is important to carefully consider these factors when deciding whether to use SAGE in your research.

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