Preparing for Genome Jumpstart…

Biology faculty member Amie McClellan and rising senior Logan Traynor have just returned from a 5-day workshop hosted by the Genomics Education partnership at Washington University in St. Louis ( Dr. Sarah Elgin, the director of the GEP program, kept them on a busy schedule of learning, primarily through hands-on training, how to use bioinformatic tools to annotate and improve regions of genome sequence.


One ultimate goal of the GEP is to demystify the apparent expression of numerous genes on the Drosophila F element, which exists in a highly condensed chromatic state.  Amie and Logan learned how to search for genes, locate introns and exons, do comparative sequence analysis amongst related species of Drosophila, and learned of the computational challenges to performing all of these tasks that thus require human eyes and intelligence.  Importantly, these experiences will feed into a new course being taught this Fall (Genome Jumpstart) in which students will actively participate in computational GEP research projects, providing an opportunity for original research and inclusion as co-authors on future collaborative publications with the GEP.

They also got the chance to tour The McDonnell Genome Institute


and enjoy some time out of their computer chairs clambering around at the City Museum (yes, they climbed all the way up into that airplane!).


When asked his thoughts on the workshop, Logan said it was “incredibly rigorous, but intensely satisfying”. Amie and Logan are both excited to implement what they’ve learned this coming Fall term in the Genome Jumpstart course!

Cell Bio students and faculty attend 20th Annual Midwest Stress Response and Molecular Chaperone Meeting


Seniors Carlos Mendez and Chernoh Jalloh traveled with faculty member Amie McClellan to Northwestern University in Evanston, Illinois, where they presented a research poster on ongoing efforts in the McClellan lab to characterize a novel Hsp90 co-chaperone.  Both Carlos and Chernoh are working on aspects of the project as part of their advanced work in biology.  They had an exciting time with their  “tag team” style poster presentation and, overall, a stimulating day of science and socializing. Amie served as the session chair for the last block of talks of the day, which focused on the organismal consequences of cellular stress. In trying to sum up the experience, Carlos said “The Midwest Meeting was great fun! I had the pleasure to learn about current research in the field to help move forward our work in the lab, as well as network with professors and graduate students in order to prepare for my upcoming graduate school interviews.” Chernoh added, “The conference was a great way for me to connect what we learned in the protein biology class last term to ongoing research in the field. Virtually every project presented at the conference had a root from the topics we covered in class, so it was refreshing to see the different angles that researchers are taking to investigate concepts that we had already discussed with Amie.”  Learn more about the meeting here:

(posted for Amie McClellan)

Science Workshop: Using Crystal Age and Compositions to Understand How Volcanoes Come Back to Life

Science Workshop:  November 7, 2014.  1 PM.  Dickinson 232.

This Friday’s Science Workshop speaker is Erik Klemetti, Assistant Professor of Geosciences at Denison University, and author of the popular Eruptions blog at Wired.

ChaosCragsHis talk, “Using Crystal Age and Compositions to Understand How Volcanoes Come Back to Life” is described as follows:

Volcanoes spend most of their existence not erupting. This doesn’t mean that there aren’t a multitude of magmatic processes going on underneath. These might include intrusions of new magma, crystallization of existing magma, magma mixing and movement of crystals through the “crystal mush” that sits under the volcano. These processes all leave their compositional and temporal signature on the crystals that form and are subsequently incorporated into the magma that does erupt. I will discuss how examination of zircon crystals in magma can help us unravel the timing and nature of events that occur between volcanic eruptions with a focus on the evolution of the Lassen Volcanic Center in California. Overall, current trace element and U-Th disequilibria age data derived from zircon suggests that an otherwise moribund magmatic system can be brought back to life (rejuvenated) by new intrusions of magmatic that are geologically ephemeral, lasting years to millennia. This conclusion means that the events that lead to the 1915 eruption at Lassen Peak unfolded rapidly before the explosive eruption, the only to occur in California in the last century.

Mechanistic Insight Into Cellular Functions and Disease States


Mechanistic Insight Into Cellular Functions and Disease States

OdonnellOur science workshop speaker for Friday, October 24th will be John O’Donnell, who is currently a PhD student in the laboratory of Holger Sondermann at Cornell University (  His talk will focus on elucidating the molecular mechanism of the protein atlastin, which is responsible for endoplasmic reticulum membrane fusion. Obtaining the blueprints of this enzyme’s function has enabled him to address questions surrounding atlastin’s contributions to cellular functions and associated disease states such as the neurodegenerative disorder Hereditary Spastic Parapalegia (HSP).


Congratulations Graduates!

This year was another productive year for Computer Science at Bennington. Students successfully implemented a distributed file system; spent Field Work Term at Nebula in Seattle (under the supervision of Ben Broderick-Phillips ’13), and CRA in Cambridge (where Erick Daniszewski ’14 will be working after graduation); and built a (nearly functional) operating system using C and ARMv6 assembly from the ground up for the Raspberry Pi.

Introductory students built an alternative source code repository to GitHub (codenamed Reposaurus), while students in Computing in the Developing World designed physical enclosures for wireless mesh network nodes and built prototype mobile apps for the developing world.  In collaboration with astronomer Hugh Crowl, we assisted in building a small radio telescope; while we also collaborated with technologist Guy Snover to use Python and Rhino 3D to create robotically-generated wall drawings and sculpture installed on campus.  It was a busy year.

But perhaps the most significant accomplishment of the year was our re-creation of some old-timey computer science photos on the last day of classes.  I’ve never grown a mustache before, and may never do so again – however, I think we nailed it overall.


Computer Scientists Gilbert-Espada, Cencini and Daniszewski with their new portable microcomputer, a Kaypro II running CP/M.


Some members of the Bennington Computer Science Laboratory, clockwise from left: Logan Traynor, Klemente Gilbert-Espada, Torrent Glenn, Andrew Cencini, Brendon Walter, Erick Daniszewski.

Congratulations and good luck to all of the graduating seniors this year!  Have a great summer!  Great things to come in the coming year!


Ben Broderick-Phillips ’13 at OpenCompute

Ben and Andrew @ OCP

Ben Broderick-Phillips (’13) and Andrew Cencini (faculty) caught in a rare moment of being dressed well.

About two weeks ago, I traveled to San Jose, CA for the OpenCompute summit – a gathering of people working on open-source data center hardware and software.  It was a good event, and my friend Steve White and I did a brief introduction to the hardware hackathon that took place there (we submitted winning entries in previous years, so we sat this one out).

But perhaps one of the most exciting things was running into Ben Broderick-Phillips (’13) at the conference.  Ben is currently working as a software engineer for Nebula, and doing great work.  He was showing off some cool and groundbreaking work that he has been doing at Nebula, and by all accounts has been helping to give Bennington a good name in the technology industry.  Hopefully, we will see Ben on campus some time this spring.

Another Hardware Hackathon Win

Cheesy Fingers installed in a Facebook OpenCompute server

On June 19th, I traveled to Facebook headquarters to compete in the second OpenCompute hardware hackathon.  The team was comprised of Steve White, Dave Kaplin and Matt Gambardella of Nebula, as well as myself.  Our previous entry won the first hardware hackathon, and involved wireless server debugging (it was called Cheesy Fingers).  Since then, Cheesy Fingers has entered production, and we were even able to test it out in a Facebook server!

Our entry this time was a wireless server debugging aggregator – basically, a device that hooks up to our wireless mesh network and sends and receives data to and from the servers in a data center rack.  We built the device, codenamed “Big Cheese” on top of the popular Raspberry Pi single-board computer. Continue reading

Scenes from Make Me Dangerous

This spring, I’m teaching an intensive introductory computer science class called “Make Me Dangerous,” where students learn computational thinking skills, Python programming, how to use Unix, and a variety of topics from the various nooks and crannies of the discipline.

Today was “hands-on hardware day (part I)” for the class, where students disassembled and explored a variety of computers and computing equipment.  Through this exercise, students became familiar with the various hardware components in a computer, and formulated some great questions on how computers work at a more fundamental level (for example, how the quartz crystal in the system clock oscillates at a given frequency, forming the main ‘heartbeat’ of the computer as it fetches and executes instructions for programs and the operating system).  We also looked at memory hierarchy, talked about how operating systems manage hardware resources, and discussed various evolutions in the hardware space.

Hardware we dissected included:  a Sun SPARCstation 5, a raspberry pi, a 300 baud modem, 3 dell desktops of various configurations, and an older dell laptop.

In addition, last week, the class went over to one of the the video studios in VAPA to take pictures in front of a green screen.  They then wrote Python programs to remove the green pixels, and replace them with an alternate background.  The class has been learning programming and computing using an approach called media computation, where students write programs to create and manipulate images, sounds and video while learning core concepts of programming.  It has been an interesting approach and has allowed for a lot of fun projects like green screen day!

OpenCompute Hardware Hack

This past week, I traveled to Santa Clara, CA to participate in the OpenCompute Summit.  OpenCompute is an open-source hardware project that aims to democratize the world of data centers (the places full of hundreds of thousands of servers, where things like Facebook, Google, Bing and Twitter live) by openly sharing and evolving hardware, software and mechanical designs.

One of the more exciting things that occurred during the conference was a “hardware hackathon” where teams made up of engineers and researchers from industry and academia came up with a novel idea to contribute to the OpenCompute project (students at Purdue had previously developed a biodegradable server chassis!).  As it turns out, the team I was a part of took first place in the competition – the prize being support and funding from the OpenCompute Foundation to file a provisional patent application for our idea, which also becomes a new mainline project as part of OpenCompute.

Visualization of our team’s component (CAD by Jon Ehlen of Facebook)

The idea that we developed was a true interdisciplinary approach to the problem of management and monitoring of servers in data centers.  We combined electrical engineering, mechanical engineering, software engineering and computer science to come up with a design for a module (codenamed “Cheezy Fingers” – long story…) that plugs into the debug header of an OpenCompute motherboard, and uses a hyper-local low-power wireless mesh network to transmit sensor, location and status data about servers, as well as to provide a mechanism for locating, identifying, and gaining remote access to the serial console of a server.   The design is based on what we know of the challenges Facebook has in managing their OpenCompute-based servers (hundreds of thousands of them), and is designed to be a low-cost, low-power component that can be easily snapped-in as a retrofit to their existing servers, as well as to any other OpenCompute server in the wild.

Our team hard at work (Jon Ehlen, Facebook; Andrew Cencini, Bennington College; David Kaplin, Nebula; Steven White, Nebula). Photo by Jill Juarez.

We had about 12 hours to discuss, evolve, and model our design – though we had also been discussing the idea in advance.  Our team was made up of two electrical engineers from Nebula – Steven White and David Kaplin, myself (the computer scientist/software guy), and Facebook’s mechanical engineer in charge of storage design, Jon Ehlen.  We had a blast working together – Jon built a beautiful CAD model of “Cheezy Fingers” in SolidWorks (see picture above), and Steven and David specced out the components and schematics.  For my part, I specified the data protocol and aggregation design, as well as wrote some C code for the serial connection that will run in the Linux kernel to retrieve locational information and blink the chassis LED using IPMI.  The judges remarked on what a thoughtful and complete submission we had – especially given it’s something we could begin mass-producing within the next 24 hours or so.

All in all, it was a great time, and a fun way to bring together people from a variety of disciplines and backgrounds to solve a real problem and make a real and meaningful contribution to the open source hardware community.  Ben Broderick-Phillips and Pratham Joshi are currently spending their FWT working on other projects with Nebula, which are slated to become contributions to the OpenCompute project as well.  Look to hear more about their work in the near future…

Update 1/21/2013: Some nice media coverage of our project here.

Update 1/24/2013:  Welcome GigaOm readers!  (GigaOm story here).