Home » Uncategorized » Faster Optimization Algorithms and Background for RevBio/ Universal Debugger

Faster Optimization Algorithms and Background for RevBio/ Universal Debugger

Lee et. al., A Faster Cutting Plane Method and its Implications for Combinatorial and Convex Optimization, here.

With the best general-purpose cutting-plane method, the time required to select each new point to test was proportional to the number of elements raised to the power 3.373. Sidford, Lee, and Wong get that down to 3.
But they also describe a new way to adapt cutting-plane methods to particular types of optimization problems, with names like submodular minimization, submodular flow, matroid intersection, and semidefinite programming. And in many of those cases, they report dramatic improvements in efficiency, from running times that scale with the fifth or sixth power of the number of variables (n5 or n6, in computer science parlance) down to the second or third power (n2 or n3).

Erika Check Hayden, nature, Why biomedical superstars are signing on with Google, here.

Mega’s decision to move in March to Google was one in a string of announcements by top-flight scientists and physicians who are enlisting in the mission, and pioneering a new type of career path in the process. Although academic researchers from fields such as computer science and engineering have led innovative Google projects (such as the Internet-connected eyewear known as Glass), Google and other technology companies are increasingly recruiting life scientists as Silicon Valley broadens its reach into health care. “I have a feeling we’re going to see a lot more recruitment of leading lights,” says Eric Topol, director of the Scripps Translational Science Institute in La Jolla, California.

In September, Thomas Insel, director of the US National Institute of Mental Health in Bethesda, Maryland, announced that he would soon be joining Google’s life-sciences company to help develop ways to apply technology in mental health. And last year, molecular biologist Cynthia Kenyon, a leader in ageing research at the University of California, San Francisco, joined the Google-backed biotech company Calico in San Francisco, California.

Quantitative Genomics, MITOpenCourseware, here.

Cambridge Computational Biology Institute, here. RevBio could still be open. Turing couldn’t do it because he didn’t have the object code (e.g., DNA sequencing). Much of the MoBio literature is descriptive – even the small amount of quant bio papers I have scanned. It’s possible most folks are working on the Grand Slam sized stuff ( better understanding evolution, etiology of disease).

We are living in a very exciting time for biology: whole-genome sequencing has opened up the field of genome scale biology and with this a trend to larger-scale experiments. However it is also a time of great opportunity for small-scale biology as there is a new wealth of data to build from: one can turn to a computer to ask questions that previously might have taken months to answer in the laboratory. One of the great challenges for the field is analysing the large amounts of complex data generated, and synthesising them into useful systems-wide models of biological processes. Whether operating on a large or small scale the use of mathematical and computational methods is becoming an integral part of biological research.

Cell Division, Mitosis, and Meiosis, here.

Core Concepts:

All Organisms Consist of Cells and Arise from Preexisting Cells
Mitosis is the process by which new cells are generated.
Meiosis is the process by which gametes are generated for reproduction.
The Cell Cycle Represents All Phases in the Life of a Cell
DNA replication (S phase) must precede mitosis, so that all daughter cells receive the same complement of chromosomes as the parent cell.
The gap phases separate mitosis from S phase. This is the time when molecular signals mediate the switch in cellular activity.
Mitosis involves the separation of copied chromosomes into separate cells
Unregulated Cell Division Can Lead to Cancer
Cell-cycle checkpoints normally ensure that DNA replication and mitosis occur only when conditions are favorable and the process is working correctly.
Mutations in genes that encode cell-cycle proteins can lead to unregulated growth, resulting in tumor formation and ultimately invasion of cancerous cells to other organs.


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