smd4's comments

smd4 | 8 years ago | on: Watching Larry Ellison Become Larry Ellison (2014)

I laughed when I read that Ellison often said, “It’s not enough to win—all others must fail.”

Once, in the early days of the field of synthetic biology, I asked my mentor George Church why he collaborated with so many people who weren't obviously doing the highest caliber work. He replied, "When you're involved in starting a new field, often it's not enough to succeed by yourself. Sometimes you also have to help others not fail."

smd4 | 8 years ago | on: Ask HN: Who is hiring? (June 2017)

Douglas Lab at UCSF (http://bionano.ucsf.edu/) | Software Developer | San Francisco, CA | REMOTE SALARY:80k-120k

Our biomedical research lab is developing software tools for the nascent field of bionanotechnology. Our long-term goal is to develop targeted cancer therapeutics. To that end, we are learning to repurpose and engineer life's building blocks (DNA, RNA, proteins) to create atomically precise nanostructures that self-assemble into prescribed shapes and devices.

We are seeking a full-time software developer to help extend our computer-aided design tool Cadnano (http://cadnano.org/) with several new features, in particular, 2D and 3D views for designing biomolecules as well as integrating structural data derived from cryo-EM and molecular dynamics simulation. Experience with PyQt and 3D CAD/CAM preferred.

We work at the interface of molecular biology, biophysics, and computer science. Biology knowledge is not required, but the position offers an excellent opportunity to learn about biotech, synthetic biology, and related disciplines.

Apply at https://goo.gl/forms/ZeZxikT8YtZ5Xfj92

smd4 | 9 years ago | on: Alan Kay has agreed to do an AMA today

Hi Alan - the innovation from PARC appears to be the result of a unique confluence of hardware, software, market forces, recent government research investment, and Michelangelo-level talent for bringing big ideas to fruition.

Do you think that any factors that were significant back then are going to be difficult to reproduce now, as HARC gets started? Conversely are there novel aspects of today's environment that you wished for at PARC?

smd4 | 10 years ago | on: Google Wins Appeals Court Approval of Book-Scanning Project

I just got into book scanning ~6 weeks ago. I was partly inspired by the August HN discussion of Jason Scott's rescue mission of 25k manuals [0], and intrigued by Jason's kind warning to "the next person to mention the Linear Book Scanner (a prototype that destroys books)".

Emeritus community hero Daniel Reetz spent 6 years creating the "Archivist" scanner [1]. He and his collaborators have done a phenomenal job, and created some of the best documentation I've seen for any project (open-source or otherwise). The "Lessons Learned" front matter alone is inspiring [2].

So far I've found that book scanning is an ideal "DIY" project: enough hardware & software quirks that are gratifying to puzzle through, but nothing super difficult. In fact, it is exactly like building and calibrating a simple scientific instrument and learning to collect and process image data. To @planfaster or anyone who is considering book scanning for private use, definitely do it!

I highly recommend buying the "Archivist" scanner kit + electronics pack available at http://tenrec.builders/. There is ample hard-earned wisdom in the forums and tenrec supplemental docs about dozens of minor process details where you think "Why don't people just do X?" and it turns out X isn't ideal, and neither is Y, but Z works fine.

The main thing that I didn't consider before starting was that the scanner hardware only facilitates one very specific part of the workflow: taking pictures of flattened pages with (nearly) identical resolution and positioning. It's an important step, and reducing it to 5 seconds per page doesn't magically eliminate tedious downstream processing with other tools[3]. All that said, it's very rewarding, and really fun to start thinking about what you can do with scans, e.g. turn entire books into posters [4].

[0] https://news.ycombinator.com/item?id=10070529

[1] http://www.wired.com/2009/12/diy-book-scanner/

[2] http://www.diybookscanner.org/archivist/?page_id=25

[3] http://scantailor.org/

[4] https://twitter.com/smd4/status/655092522071420929

smd4 | 12 years ago | on: Visualizing Git Concepts with D3.js

The best resources I've found for understanding git workflows are by Vincent Driessen[1] and Atlassian[2].

The Atlassian page is much more comprehensive, and in fact derives the 'GitFlow' workflow from Driessen. However, I prefer his original top-to-bottom representation (a left-to-right time axis seems less intuitive to me - they remind me of a football playbook rather than a waterfall).

[1] http://nvie.com/posts/a-successful-git-branching-model/ [2] https://www.atlassian.com/git/workflows

smd4 | 12 years ago | on: Visualizing Git Concepts with D3.js

Nice work!

This is a great complement to the codeschool tutorial [1] it would be nice similarly offer the feature that clicking on the command will auto-populate the virtual terminal. New git users might be more likely to use a client-side GUI where they are clicking buttons rather than typing in the terminal.

[1] http://try.github.io/

smd4 | 12 years ago | on: How Academia and Publishing are Destroying Scientific Innovation

Hey, don't despair.

First, not everyone has admitted defeat. Maybe you just need to meet more people. Grad schools are just wrapping up admission season, and I'm totally inspired by the level of talent and quality of students I met this past few months.

Second, scientists are among the greatest beneficiaries of the information technology revolution. The most important instrument every scientist uses is a personal computer. Brenner says "The way to succeed is to get born at the right time and in the right place. If you can do that then you are bound to succeed. You have to be receptive and have some talent as well." This definitely feels like the right time and place to me.

Science may be the pursuit of knowledge, but that doesn't mean humans who work as scientists get to be privileged when it comes to allocation of resources. We will just have adapt to new ways of communicating why our work is important, and new ways of raising money [1]. Science is way more expensive than most people realize, but it costs millions, not billions to run a successful lab.

Anyway, we'll make it work. Just like our predecessors made it work when science budgets were a fraction of their current size.

[1] For example: YC-backed experiment.com

page 1