Coding for Medicine for High School

Announcement: RESEARCH TALK on SUNDAY, APRIL 27, 3 pm PST (5 pm CST/6 pm EST)

The 2024 summer research cohort will present their research work on Sunday, April 27.

TITLE: Comparative Analysis of Plastid Genomes in Flowering Plants Using Pangenome Research ToolKit (PGR-TK)

SPEAKERS: Hannah Beaver, Aaron Beaver, Aadhavan Veerendra and Aditya Vinukonda (Team Talk)

For Zoom link please register here: https://forms.gle/ZZ4UNVcGpAsfLhwh9

This is an open talk (not limited to Coding For Medicine students/clubs), so please feel free to share with peers and friends who may also be interested.

Direct Link to Summer Modules

Introductory Coding for Medicine (online)	Introductory Coding for Medicine (in person)	Intermediate Coding for Medicine(online)	Summer Research
Machine Learning & AI -1 (online)	Learning Chemistry with Enzymes (Lab)	Microbial Mysteries (Lab)	Yearlong Puzzles

MAJOR NEWS/UPDATES FOR 2025

Machine Learning and AI Modules: This year, we have two new modules on AI and machine learning using Python. This topic was the top suggestion in your feedback form last year. We are also again offering the two lab modules - "Learning Chemistry from Enzymes" covering the concepts of chemistry based on biochemical molecules and "Microbial Mysteries" on biotechnology. These lab classes will be held at the Bellevue college. For coding topics, both in-person classes at Bellevue College and online classes thorugh zoom will be offered so that the students from around the country can join.

Research Module: This year we are again offering the summer-long independent research program, but with one important modifications from the last year. This time, we are extending the time to Sep 30 so that the students get sufficient time to complete their research reports. We understand that the schools will start by then, but the students should have their projects completed by mid-Aug and can spend the last month in polishing up the report. For this module, we plan to have a small group of students selected based on merit and genuine interest. Please contact us for more details.

Self-learning Modules: We are also creating self-paced video versions of many of our popular modules, which will be available online in the coming weeks and months. This allows you to learn at your own convenience without having to wait for the summer. For instance, our "Calculus Meets Coding" module, which teaches R and calculus, received excellent feedback from the students. However, we often struggle to schedule this module every summer, so the new video format offers a flexible solution.

Science Fair Top Award and Papers: Over the last summer and fall, students from our research groups did fantastic work in understanding the taxonomy of plants using pangenome analysis programs. Dr. Samanta is in the process of writing the papers, which will be available soon. In a separate project, Defne Dingiloglu from Tesla STEM High School looked for antibiotic and antitumor secondary metabolites in the bacteria Streptomyces scabiei under the guidance of Dr. Samanta and received the first place in computational biology category at Washington State Science and Engineering Fair (WSSEF). You can see her report here.

Yearlong Module: This has been an exciting year with our yearlong problem solving modules. Students can join this self-paced module any time. Each of them gets one question at the beginning of the month and then the solution at the end of the month. Dr. Samanta has been meeting the students every month through zoom. Also, we continue to improve the videos and texts of the problems/solutions based on the student feedbacks.

News from prior years -

High-school Clubs: Coding for Medicine clubs are expanding rapidly. In 2020, Leo Zou and Athulya Saravanakumar, our students from the Dulles High School in Sugarland, TX, started a Coding for Medicine club at their school. Today four more student-run Coding for Medicine clubs are operational in various high shcools, and several more clubs formed by students from our summer program are in their planning stages. If you are interested in starting a Coding for Medicine club at your school, let us discuss.

Research by Anne Grodjak: Anne Grodjak, our student from 2017, conducted excellent research for two years under the supervision of Dr. Samanta and reported the findings in this paper. Anne joined MIT in the fall of 2021.

Coding for Medicine in its Eleventh Year

Coding for Medicine is an innovative organization dedicated to teach coding skills to young people based on real-life problems. Our primary areas are biology and medicine, but we also offer interesting modules like "Precalculus Meets Coding" and "Calculus Meets Coding" to teach precalculus/calculus and coding together, and "Catching Pokemons with Coding" to teach coding to the middle-school students.

Our highly favoured high-school summer camps are in eleventh year now. Over the years, we expanded to many topics and areas. The years 2018-2021 had been particularly exciting.

Anne Grodjak, our student from 2017, conducted excellent research for two years under the supervision of Dr. Samanta and reported the findings in this paper. Anne joined MIT in the fall of 2021.

In 2020, Leo Zou and Athulya Saravanakumar from the Dulles High School, Houston, TX started a Coding for Medicine club for their school to introduce their fellow students to biology-inspired coding. This club had been a great success. If you are interested in starting a similar club at your school, please contact us.

In addition to the coding camps, we introduced a biotechnology lab module ("Tinkering with DNA") in 2018 and continued with "Microbial Mysteries" lab in 2019 to explore the microbial world. After a break due to covid lockdown in 2020, we again offered the module in 2021 at the Redmond Ridge location. We plan to offer it again this year and are figuring out the logistics.

In the Fall of 2018, we offered the online module "Calculus Meets Coding" for high-schoolers. We continued in Fall 2019, with another online module - "Precalculus with Coding and Animation" for advanced middle-schoolers and high-schoolers. This year, we have a condensed module based on those topics.

With our students from the 2017 high-school summer camp, we raised money through crowdfunding to uncover the genetic secrets of salmonberry. Research on this project is nearly complete, and we are working on the publication.

In late 2018, we initiated online classes on R and bioinformatics for college students and post-doctoral researchers.

Introductory Coding for Medicine (online with live instructor)

This hands-on module introduces you to the Python programming language through a series of problem-solving exercises. It also covers key aspects of the Linux operating system, provides guidance on accessing publicly available genomic data, and demonstrates how to use the NCBI BLAST search engine for DNA sequence analysis.

Just like last year, our this year's theme is coronavirus (SARS-CoV-2). We will download its publicly available DNA sequences and and you will write code to analyze it.

Price

$395 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

June 16-20, 23-27 1-3PM PST

July 7-11, 14-18 1-3PM PST

July 28-31, Aug 1,4-8 1-3PM PST

Aug 11-15, 18-22 1-3PM PST

Prerequisites:

None. Limited to advanced middle schoolers and high schoolers.

Style:

The classes will be conducted online through zoom and interactive chat sessions.

Course Details

Register

Introductory Coding for Medicine (in person)

This hands on module introduces you to the Python programming language through a series of problem solving exercises. Additionally, you learn about the Linux operating system, where to get publicly available genomic data and NCBI BLAST search engine for DNA sequences.

Just like last year, our this year's theme is coronavirus (SARS-CoV-2). You will download its publicly available DNA sequences and write code to analyze it.

Price

$545 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

July 21-25, 10AM-3PM PST

Prerequisites:

None. Limited to advanced middle schoolers and high schoolers.

Style:

This is an in-person module to be held at the Bellevue College.

Course Details

Register
Advanced Coding for Medicine and Summer Research

This summer-long module will allow you to read scientific publications and perform independent research in bioinformatics. This year, we will look into bacterial and archaeal genomes and understand how their genomes and genes evolve. We will use the pangenome analysis tools in this effort.

This year, we are making the session go longer to last until Aug 30 (fall). Additionally, the students will spend some more time after the module to complete and publish their research reports. Unlike prior years, we will not offer any fall research module.

Over the years, we experimented with a number of approaches for this advanced module including two-week classroom-type sessions with pre-determined content more advanced than the intermediate modules or open-ended research sessions over the whole summer. Both approaches had their shortcomings, and therefore this time, we plan to take a hybrid approach.

There will be both sub-components - (A) (online) classroom sessions with pre-determined content for two weeks of the summer, and (B) open-ended independent research for the entire summer with the guidance from an instructor. In this later subcomponent, the students will be working with guidance from an instructor and group or individual meetings every week.

You are required to complete the intermediate module before joining this module. Also, because of the time commitment from both the students and the instructor, the class size is extremely limited, and the students will be selected based on merit and interest.

Price

$695

Choice of Sessions

June 15 - Aug 30 + Time for Writing Paper

Prerequisites:

Intermediate coding for medicine module

Style:

Register

Intermediate Coding for Medicine (online with live instructor)

In this hands on programming course, you will use your Python coding skills to explore genome sequences and find key genes, learn how to develop computer algorithms to analyze genomes and see the big picture of where the new cutting-edge jobs are created for the 21st century.

After starting with the small coronavirus genome, you will explore the human genome to find information.

Price

$395 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

TBD. Please suggest your preferences during summer in the registration form.

Prerequisites:

Introductory module or equivalent

Style:

The classes will be conducted online through zoom and interactive chat sessions.

Course Details

Register
Machine Learning and AI Concepts in Python (online with live instructor)

In prior years' feedback forms, many of you requested a class on AI and machine learning. This module will introduce you to the topics and give you some hands-on experience.

In the first week, it will provide an overview of fundamental machine learning concepts including regression, classification, clustering, and dimensionality reduction. Through hands-on exercises, participants will gain practical experience using the scikit-learn in Python to implement different techniques. A variety of datasets, including both biological and non-biological examples, will be explored.

In the second week, the students will also learn about the broader landscape of artificial intelligence, focusing on applications in biology and elsewhere. They will also use the Pytorch library. This module is designed to be accessible and will not delve deeply into the mathematical details except for a brief overview.

Price

$395 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

July 28-31, Aug 1,4-8, 10AM-12Noon PST

Prerequisites:

Python skills with knowledge of numpy + pandas.

Style:

The classes will be conducted online through zoom and interactive chat sessions.

Course Details

Register

Learning Chemistry from Enzymes (Lab)

The living world and the biological materials in it have been possible because of the presence of a set of proteins called enzymes. Enzymes are biocatalysts. Without them, none of the biochemical transformations will be possible and there would be no life! Indeed nature is the best chemist and exploring how enzymes work is helping chemists to understand catalysis. Enzymes accelerate biochemical reactions at tremendous speeds such as 10^17 and with high specificity and 100% yields. Incorporating more and more enzymes into our daily lives such as in manufacturing of fine chemicals, pharmaceutical products, water treatment facilities, daily chores, recycling of plastics etc holds the key to sustainable living.

In this laboratory course we will learn about enzyme-catalyzed reactions, kinetics of enzymatic reactions, enzyme stability and inhibition, enzyme purification and building enzymatic probes. The laboratory course will be supplemented by a single Zoom lecture class prior to the start of the course. The Zoom class will provide the background of the course and explain the experimental procedure in detail.

This in-person lab will be held at the Bellevue College.

Price

$650 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

TBD. Please suggest your preferences during summer in the registration form.

Prerequisites:

Style:

This is an in-person lab class to be held at the Bellevue College.

Register

Microbial Mysteries (Lab)

There is a vast untapped microbial world around us. So far our discoveries have merely scratched its surface. Large-scale genomic sequencing is providing us the opportunity of probing this world at a depth and scale never before possible.

Microbial Mysteries- a laboratory course will teach the students the skills and techniques of the biotechnology laboratory and how to use them to explore the microbial world. From learning to use the micropipettor and microscope students will grow and culture bacteria, extract genomic DNA, use PCR to amplify DNA and read sequence data.

This in-person lab will be held at the Bellevue College. It will be supplemented by a single Zoom lecture class prior to the start of the course. The Zoom class will provide the background of the course and explain the experimental procedure in detail.

Price

$625 (Bring a friend and earn an additional *shared* 10% discount (5% each person))

Choice of Sessions

TBD. Please suggest your preferences during summer in the registration form.

Prerequisites:

Style:

This is an in-person lab module to be held at the Bellevue College.

Register
Year-long self-directed module

This module helps you learn coding and biology with a new problem every month.

At the beginning of each month (depending on you starting date), you will receive problems in one of the two categories (i) a single-concept, (ii) research-type.

We will post both problems in text and video forms at the beginning of the month and post the solutions at the end of the month. You can work on the questions during the month, and if you need help, you can communicate with us using the classroom chat. Moreover, we will arrange one zoom meeting every month with all students together to discuss various questions.

Price

$199

Choice of Sessions

year-long

Prerequisites:

Knowledge of Python for 'single-concept'. Completion of intermediate module for 'research style'.

Style:

These are self-study modules with vidoe and text-based tutorials. We meet once a month with all students.

Course Details

Register