Genome Analysts

A project to help get millions of unemployed people working on what is certainly humanity's biggest (and perhaps also most important) task: understanding the secrets of life encoded in the human genome.

How to monetize? Working on it. But realize that this is a project conceived through The Art of the Long View. Though it will surely be a lot of fun, it may be a decade or longer before it starts showing measurable value.

To get involved, send email to (keep the subject intact). To tell a friend, send them an email with this link. Follow @GenomeAnalysts and @Gamonics on Twitter.

Unemployment & Data Overload

I believe we now have more genomic data than we can possibly hope to develop a holistic understanding about with even 10,000 years of research by all the world's existing genomics researchers. And I would like to see the world's ever-rising number of unemployed people learn genomics and begin trying to help understand this staggering amount of data we have already accumulated (and we're accumulating the data at ever-faster rates). As computers and robots (see minutes 23:25-26:12) put more and more humans out of work, let's get more and more humans involved in a task that computers may never do well: understanding the genome in all its seemingly unfathomable complexity.

Human Workers
Image © 02012 by Andreas Gursky (unlicensed use under 17 U.S.C. §107)

Sure, these people are gainfully employed here, but:

Baxter Robot
Image © 02012 by Rethink Robotics (unlicensed use under 17 U.S.C. §107)

Resources for Building Skills

MITx : 7.00x : Introduction to Biology - The Secret of Life

Course starts on 17 June 2014

This course was offered twice at edX in the year 02013. With more than 80,000 Likes on its Official Facebook Page and at least 2,184 graduates from its inaugural offering, it has been a huge success and is sure to be offered again. This is one of the best starting places for anyone interested in helping to understand all the secrets that are surely still hidden in the human genome. Pay close attention to the last problem set which involves the use of IGV Lite software, a simplified version of IGV (Integrative Genomics Viewer) which has been released by The Broad Institute to the public under a LGPL license.

HarvardX : PH207x : Health in Numbers: Quantitative Methods in Clinical & Public Health Research

Course last offered in late 02012, but most learning resources are still available.

From the course description: “Quantitative Methods in Clinical and Public Health Research is the online adaptation of material from the Harvard School of Public Health's classes in epidemiology and biostatistics. Principled investigations to monitor and thus improve the health of individuals are firmly based on a sound understanding of modern quantitative methods. This involves the ability to discover patterns and extract knowledge from health data on a sample of individuals and then to infer, with measured uncertainty, the unobserved population characteristics. This course will address this need by covering the principles of biostatistics and epidemiology used for public health and clinical research. These include outcomes measurement, measures of associations between outcomes and their determinants, study design options, bias and confounding, probability and diagnostic tests, confidence intervals and hypothesis testing, power and sample size determinations, life tables and survival methods, regression methods (both, linear and logistic), and sample survey techniques. Students will analyze sample data sets to acquire knowledge of appropriate computer software. By the end of the course the successful student should have attained a sound understanding of these methods and a solid foundation for further study.” Text © 02013 by edX (unlicensed use under 17 U.S.C. §107)

GeorgetownX : PHLX101-01 : Introduction to Bioethics

Course started on 15 April 02014.

From the course description: “Should we clone humans? Who owns our DNA? How much control should we have over how and when we die? When does medical treatment turn into medical enhancement — and should we care? Is rationing health care good, bad, necessary — or all of the above?

This course will explore fundamental moral issues that arise in medicine, health, and biotechnology. Get behind the headlines — and polarized debates — and join others who want to think deeply and openly about these problems. Some are as old as life itself: the vulnerability of illness, the fact of death. Some are new, brought on by a dizzying pace of technology that can unsettle our core ideas about human nature and our place in the world. And nearly all intersect with issues of racial and gender equality, as well as policies affecting the world’s most vulnerable populations.

Designed to introduce students to the range of issues that define bioethics, together with core concepts and skills, this course should be of interest to undergraduates, health care professionals, policy makers, and anyone interested in philosophy or ethics.” Text © 02014 by edX (unlicensed use under 17 U.S.C. §107)

HarvardX : PH525x : Data Analysis for Genomics

Course started on 07 April 02014.

From the course description: “Data Analysis for Genomics will teach students how to harness the wealth of genomics data arising from new technologies, such as microarrays and next generation sequencing, in order to answer biological questions, both for basic cell biology and clinical applications.

The purpose of this course is to enable students to analyze and interpret data generated by modern genomics technology, specifically microarray data and next generation sequencing data. We will focus on applications common in public health and biomedical research: measuring gene expression differences between populations, associated genomic variants to disease, measuring epigenetic marks such as DNA methylation, and transcription factor binding sites.

The course covers the necessary statistical concepts needed to properly design experiments and analyze the high dimensional data produced by these technologies. These include estimation, hypothesis testing, multiple comparison corrections, modeling, linear models, principle component analysis, clustering, nonparametric and Bayesian techniques. Along the way, students will learn to analyze data using the R programming language and several packages from the Bioconductor project.

Currently, biomedical research groups around the world are producing more data than they can handle. The training and skills acquired by taking this course will be of significant practical use for [everyone]. The learning that will take place in this course will allow for greater success in making biological discoveries and improving individual and population health.” Text © 02013 by edX (unlicensed use under 17 U.S.C. §107)

MITx : 15.071x : The Analytics Edge

Course started on 04 March 02014.

From the course description: “In the last decade, the amount of data available to organizations has reached unprecedented levels. Data is transforming business, social interactions, and the future of our society. In this course, you will learn how to use data and analytics to give an edge to your career and your life. We will examine real world examples of how analytics have been used to significantly improve a business or industry. These examples include Moneyball, eHarmony, the Framingham Heart Study, Twitter, IBM Watson, and Netflix. Through these examples and many more, we will teach you the following analytics methods: linear regression, logistic regression, trees, text analytics, clustering, visualization, and optimization. We will be using the statistical software R to build models and work with data. The contents of this course are essentially the same as those of the corresponding MIT class (The Analytics Edge). It is a challenging class, but it will enable you to apply analytics to real-world applications.” Text © 02014 by edX (unlicensed use under 17 U.S.C. §107)

GeorgetownX : MEDX202-01 : Genomic Medicine Gets Personal

Course starts on 04 June 02014.

From the course description: “While the advances in genomics promise to usher in a new era in medical practice and create a major paradigm shift in patient care, the social impact of genomic medicine will be equally significant. The information and potential use of genomic discoveries are no longer issues left for scientists and medical professionals to handle, but have become ones for the public at large. Rarely a day passes without a genomics-related story reported in the media. By the end of this course, students will be able to better understand the field of genomics; be familiar with various online databases and resources; and understand and appreciate the medical, social, ethical, and legal issues associated with the availability of personal genomic information.” Text © 02013 by edX (unlicensed use under 17 U.S.C. §107)

MITx : 7.QBWx : Quantitative Biology Workshop

Course starts on 10 June 02014

From the course description: “A workshop-style introduction to tools used in biological research. Discover how to analyze data using computational methods. Do you have an interest in biology and quantitative tools? Do you know computational methods but do not realize how they apply to biological problems? Do you know biology but do not understand how scientists really analyze complicated data? 7.QBWx: the Quantitative Biology Workshop is designed to give students exposure to the application of quantitative tools to analyze biological data at an introductory level. For the last few years, the Biology Department of MIT has run this workshop-style course as part of a one-week outreach program for students from other universities. With 7.QBWx, we can give more students from around the world the chance to discover quantitative biology. We hope that this series of workshops encourages students to explore new interests and take more biology and computational courses.

We expect that students from 7.00x Introduction to Biology – The Secret of Life or an equivalent course can complete this workshop-based course without a background in programming. The course content will introduce programming languages but will not teach any one language in a comprehensive manner. The content of each week varies. So students with programming experience will find some weeks easier than students with only biology experience, while 7.00x students should find the week on genetics easier than students without that experience. We recommend that students try to complete each week to find what interests them the most.” Text © 02014 by edX (unlicensed use under 17 U.S.C. §107)

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