The course content consists of two main parts. The first part deals with an introduction to python, the goal of which is to lay down the basics of algorithms and programming languages in general. The first part contains the following:
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The course content consists of two main parts. The first part deals with an introduction to python, the goal of which is to lay down the basics of algorithms and programming languages in general. The first part contains the following:
The course content consists of two main parts. The first part deals with an introduction to python, the goal of which is to lay down the basics of algorithms and programming languages in general. The first part contains the following:
Install python, pycharm, and biopython.
Knowledge of basic syntax, which includes variables and line write methods in python.
Knowing the five variable types, which include number, string, list, tuple, and dictionary.
Knowing the operator types, including arithmetic, comparison, assignment, logical, membership, and identity.
Understanding decision-making strategies, including the use of "if .. else", "if .. elif .. else" and "nested if.".
Understanding loops, writing, and controlling while loop and for loop.
The second part is an introduction to biopython, which is a package based on python, so we will apply what was understood in the first part. The second part contains the following:
Dealing with the NCBI database through Entrez, requires an internet connection, and we will use einfo, espell, esearch, esummary, egquery, and efetch.
Working with files, writing, and converting files using seqio. dealing with the two most popular types of sequence files in terms of reading and writing in detail.
Working with sequences through python, they understand some functions such as slice, find, count, len, lower, upper, replace, split, join and strip.
Transcription of molecules as cell, transcription and reverse transcription of DNA and RNA respectively, DNA translation. manufacture of complement and reverse complement of DNA.
Simple basic analysis of sequences, including GC content, molecular weight, and six reading frames. search inside sequences using nt_search.
Pairwise alignment, understanding, and implementing both local and global alignment. work with results and understand matches and gaps.
Multiple sequence alignment, execute and read multiple sequence alignment and extract data for the phylogenetic tree.
Blast, sequence search in the NCBI database. build a local database and implement blast offline. dealing with results in detail.
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Activities
Connect with experts in the field of bioinformatics
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Establishing connections with experts can provide invaluable guidance and support throughout your bioinformatics journey.
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Mentorship
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Attend industry events and conferences.
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Reach out to professors, researchers, or professionals in the field.
-
Request informational interviews or mentorship opportunities.
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Maintain relationships and seek ongoing guidance.
Create a comprehensive study guide
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Compiling a study guide will help you synthesize and organize course materials for effective exam preparation.
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Exam Preparation
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-
Gather all course notes, assignments, and resources.
-
Identify key concepts, definitions, and formulas.
-
Organize the material into logical sections and subsections.
-
Summarize and condense information in a clear and concise manner.
-
Review the study guide regularly and test your understanding.
Solve Python coding challenges
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Engaging in practice drills will reinforce your understanding of Python syntax and algorithmic concepts.
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Python Programming
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Register for an online coding platform.
-
Choose a set of coding challenges aligned with the course topics.
-
Attempt to solve the challenges independently.
-
Review solutions and discuss approaches with peers or instructors.
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Participate in online discussion forums
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Engaging in discussions will foster collaboration, clarify concepts, and expose you to diverse perspectives.
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-
Join online discussion forums related to the course topics.
-
Participate in discussions, asking questions and sharing insights.
-
Review and comment on others' posts.
-
Summarize key points and insights gained.
Follow tutorials on bioinformatics tools
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Tutorials will provide hands-on experience and supplement the course materials on bioinformatics tools and databases.
Show steps
-
Identify reputable online resources or tutorials.
-
Select tutorials relevant to the course content.
-
Follow the instructions and complete the exercises provided.
-
Document your findings and share insights with classmates.
Develop a data visualization for sequence analysis
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Creating a data visualization will enhance your ability to interpret and communicate complex sequence analysis results.
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Data Visualization
Show steps
-
Choose a dataset from the NCBI or other public databases.
-
Analyze the data and identify patterns or trends.
-
Select an appropriate data visualization tool.
-
Create a visually appealing and informative visualization.
-
Share your visualization and explain your findings.
Build a local BLAST database
Show steps
Constructing a local BLAST database will provide hands-on experience with advanced sequence analysis techniques.
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Blast
Show steps
-
Acquire sequence data from the NCBI or other databases.
-
Format the data into a FASTA file.
-
Use the BLAST+ command-line tools to create the local database.
-
Run BLAST searches against your local database.
-
Interpret and analyze the search results.
Contribute to a bioinformatics open-source project
Show steps
Contributing to open-source projects will enhance your understanding of bioinformatics tools and best practices.
Show steps
-
Identify a bioinformatics open-source project that aligns with your interests.
-
Familiarize yourself with the project's codebase and documentation.
-
Identify areas where you can contribute improvements or new features.
-
Submit your contributions for review and merge.
-
Participate in discussions and collaborate with other contributors.
Connect with experts in the field of bioinformatics
Show steps
Establishing connections with experts can provide invaluable guidance and support throughout your bioinformatics journey.
Browse courses on
Mentorship
Show steps
- Attend industry events and conferences.
- Reach out to professors, researchers, or professionals in the field.
- Request informational interviews or mentorship opportunities.
- Maintain relationships and seek ongoing guidance.
Create a comprehensive study guide
Show steps
Compiling a study guide will help you synthesize and organize course materials for effective exam preparation.
Browse courses on
Exam Preparation
Show steps
- Gather all course notes, assignments, and resources.
- Identify key concepts, definitions, and formulas.
- Organize the material into logical sections and subsections.
- Summarize and condense information in a clear and concise manner.
- Review the study guide regularly and test your understanding.
Solve Python coding challenges
Show steps
Engaging in practice drills will reinforce your understanding of Python syntax and algorithmic concepts.
Browse courses on
Python Programming
Show steps
- Register for an online coding platform.
- Choose a set of coding challenges aligned with the course topics.
- Attempt to solve the challenges independently.
- Review solutions and discuss approaches with peers or instructors.
Participate in online discussion forums
Show steps
Engaging in discussions will foster collaboration, clarify concepts, and expose you to diverse perspectives.
Show steps
- Join online discussion forums related to the course topics.
- Participate in discussions, asking questions and sharing insights.
- Review and comment on others' posts.
- Summarize key points and insights gained.
Follow tutorials on bioinformatics tools
Show steps
Tutorials will provide hands-on experience and supplement the course materials on bioinformatics tools and databases.
Show steps
- Identify reputable online resources or tutorials.
- Select tutorials relevant to the course content.
- Follow the instructions and complete the exercises provided.
- Document your findings and share insights with classmates.
Develop a data visualization for sequence analysis
Show steps
Creating a data visualization will enhance your ability to interpret and communicate complex sequence analysis results.
Browse courses on
Data Visualization
Show steps
- Choose a dataset from the NCBI or other public databases.
- Analyze the data and identify patterns or trends.
- Select an appropriate data visualization tool.
- Create a visually appealing and informative visualization.
- Share your visualization and explain your findings.
Build a local BLAST database
Show steps
Constructing a local BLAST database will provide hands-on experience with advanced sequence analysis techniques.
Browse courses on
Blast
Show steps
- Acquire sequence data from the NCBI or other databases.
- Format the data into a FASTA file.
- Use the BLAST+ command-line tools to create the local database.
- Run BLAST searches against your local database.
- Interpret and analyze the search results.
Contribute to a bioinformatics open-source project
Show steps
Contributing to open-source projects will enhance your understanding of bioinformatics tools and best practices.
Show steps
- Identify a bioinformatics open-source project that aligns with your interests.
- Familiarize yourself with the project's codebase and documentation.
- Identify areas where you can contribute improvements or new features.
- Submit your contributions for review and merge.
- Participate in discussions and collaborate with other contributors.
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Bioinformatics Scientist
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Biostatistician
Data Scientist
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Research Scientist
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