That’s a graph automatically generated by the cell signalling pathway simulation automation software I developed over the winter break. It’s a bit ugly — a quick and dirty CDF rendered in R of activation times of ERK in the TCR (T-Cell Receptor) pathway model for a particular endogenous pMHC ligand dosage. Fancy lingo, eh?

The past several weeks I participated in CMACS, an NSF-funded program intended to get undergrads to go on to grad school. You mean I’m not in grad school yet? Oh, right. More on CMACS later. I joined the Treespace research group at Lehman, where I’ll be expanding on my limited knowledge of phylogenetics and drawing some pretty graphs with Java, Python, and Cytoscape. I continue to be involved at Hunter with the EvoBioLab where I’m reading up on bacterial recombination and mutation and working on genomic visualization tools. The hackerspace I started back in September is thriving, with fifteen paying members, and we just filled up a 100 seat event we’re hosting at the NYPL. I’m working on organizing an iGEM team at Hunter and looking into starting some of that work at Genspace — we already have a rather nice team lineup. I hope to continue the work I started this past summer with my esteemed colleague James Estill. Yes, I’ll be taking some classes, too. Organic chemistry included. What, me nervous? Back to CMACS…

We looked at cell signalling pathways in cancer using stochastic simulations in BioNetGen. I got a bit carried away automating experiments and created ScanBatch. This new tool I whipped up runs arbitrary numbers of simulations over arbitrary numbers of models, species (molecule types), and concentrations of those species. To my delight, I’ve been asked to contribute ScanBatch to the BioNetGen project and continue work on it to expand the automated simulation capabilities. I’ll be working on accepting more complex parameter ranges, templating the simulation code, doing more complex combinations of parameters, validating model output, and making large batches of simulations scale. It’s an honor to be asked to help take such a cool piece of cutting edge research software to the next level. I look forward to working with Dr. Jim Faeder and co. on this. I’m digging Systems Biology!

If everything I’m working on pans out, I can expect to see my name on a few papers next year, which would be concrete proof that this whole scientist thing is really happening. I’ve been getting paid to do science related work since June 2011, and it’s a good feeling that this trend is ongoing. It was only months before that I threw down the gauntlet and challenged myself to do only science work. I’m feeling a strong pull towards systems and synthetic biology, but I may be biased since I’m a computer programmer, and the field seems to be especially welcoming towards my kind right now. I hope you, my friends, family, and colleagues, have had a wonderful and imagination-catalyzing winter so far.

PS. Convergence of ideas: Bacterial evolution simulation at EvoBioLab, Bacterial recombination as engine for computation in-vivo for combinatorial problems. Bacterial evolution of whole genomes plus gene expression simulation via BioNetGen. Visualization of genomic data, visualization of phylogenetic data, visualization of cell pathway data. DNA fingerprinting, DNA computing, cryptography and digital security. Okay, now I can sleep.

My first experiments (here and here) are simplistic, but pleasant, I think. My initial goal was to squeeze a nice big chunk of DNA into a small space. To that end, I more or less succeeded with the spiral approach. It turns out (unsurprisingly) that the circular visualization of genomic data isn’t new, though I don’t know if anyone has used my particular approach. Visualization is an exceedingly fun thing to poke at and learn, and I look forward to coming up with more ways of making functional bio-art.

On the practical side of things, Dr. Qiu and my colleagues at the evolutionary bioinformatics lab have been enlightening me to the professional needs of biologists in the realm of visualization. Some of the things I’ve been advised to look into are: six frame translation, SNPs, GC base percentages, amino acid frequency, synteny (gene order), genetic drift, real time simulation visualization, and phylogeny. That’s quite a laundry list. One must be careful when asking for ideas and suggestions in the lab.

Six frame translation refers to the six ways to look at a DNA sequence — three forward and three backward. There are three in each direction because the DNA is broken up into codons that each have three bases. It’s impossible to know which base a gene starts on without trying all three in either direction. So, you look for long uninterrupted sequences of codons (an open reading frame, or ORF), at each of the six reading frames. Those could quite possibly be genes, and finding a gene is like striking gold.

Here’s my rendering of reading frame 1 on the same Borrelia plasmid. I’m nearly 100% sure that I got something wrong, because when I checked ORF Finder, I got different results. This is a demonstration of the concept for a tool for finding potential genes, like the NCBI orf finder. The coloring of the segments is exponentially scaled based on size, and they become delimited by a blue border when they reach a maximum threshhold. In other words, the red areas with a blue border are most likely to be genes. It’s basically a heat map for genes. Well, so goes the theory, in my limited understanding. I’m hoping to fix this up so that I get results consistent with NCBI for all reading frames.

I’m rendering these in 100% homegrown convoluted OpenGL/C++ code. Ultimately I suspect that any general purpose genome visualization tool I might end up with will want to live on the web, perhaps utilizing WebGL. Even if this turns out to be a command line tool, it could live on the web as an image generator. For the moment, I’m enjoying developing natively on my laptop as an idea scratchpad. Before I go implementing any more features, I’ll make sure the sequence data is coming through accurately so that the ORFs match NCBI. Then I’ll tackle six frame alignments, etc. At that point, hopefully I’ll have something worth sharing!

Any thoughts on genome visualization? Suggestions? Please leave a comment.

The first law of thermodynamics states that energy can only change forms but cannot be created or destroyed. The energy used to power the pumps becomes stored as the charge differential between the inside and outside of the cell. When that differential is removed by the flow of positive ions into the cell, the stored energy is released in the form of small waves. Like little waves combining to create big waves in the ocean, as thousands of neurons fire, the little waves come together to create the larger waves knows as brain waves. It is these dominant brainwaves that are measured by NeuroSky devices.

Here I’m at Hack Manhattan viewing brainwave data from a NeuroSky MindSet EEG device on my thinkpad running Ubuntu. Puzzlebox open source software  provides a good starting point for hacking EEG technology.

While you can’t decipher genetic code directly with these technologies, DNA sequencers which pump out the actual discrete code of DNA are built on these two foundational technologies. Alone, PCR and electrophoresis can be used to do meaningful genetic and forensic analysis.

PCR:

OpenPCR raised $12,000 on kickstarter to produce a $600 PCR kit made from a lasercut plywood frame with a 16 well plate and PC based controls. Open source (cad, eagle, source code available).

Coffee cup PCR is an impressive DIY project posted on Instructables that appears to be made by a student research group out of RIT, but I’m not entirely sure. Features PC controls using a proprietary heat controller.

Lighbulb PCR is a project by biohacker Russell Durrett which uses an arduino controlled lightbulb to thermocycle pcr tubes. The housing is made from PVC pipe and air is circuled with a PC fan. Open source.

Gel electrophoresis:

Cheapass gel box is a project by Joseph Elsbernd for a working gel box made for $21. The enclosure appears to be a $2 box.

Mini Gel electrophoresis system is an Instructables project posted by Joanne C. Long which describes a rather nice looking gel box design that can be built for $50-80. The enclosure is a professional looking set of laser-cut acrylic parts.

Open Gel Box 2.0 is a community effort to design an open source gel box. It culminated in kit and assembled gel box offerings from the company Pearl Biotech. Some design files are available.

Low cost DNA gel documentation is an article by Nick Oswald that describes a project to do affordable digital photography of stained gels. A comment left by Dan Rhoads reads “You don’t even need the UV transilluminator. If you’re using sybr Green or sybrSafe, you simply use blue LEDs like a bicycle lamp or a strong torchlight.”

It’s worth mentioning umbrella project OpenWetWare which is a driving force for open source community effort in biotech. If you’re looking for DIY bio stuff, that’s a good place to start. You’ll also want to check out the DIYBIO site and join the global and regional discussion groups (mailing lists).

I’ve almost certainly missed any number of promising DIY projects, so please send them along if you’re aware of any. Happy biohacking!

We have a civilization based on science and technology, and we’ve cleverly arranged things so that almost nobody understands science and technology. That is as clear a prescription for disaster as you can imagine. While we might get away with this combustible mixture of ignorance and power for a while, sooner or later it’s going to blow up in our faces. The powers of modern technology are so formidable that it’s insufficient just to say, “Well, those in charge, I’m sure, are doing a good job.” This is a democracy, and for us to make sure that the powers of science and technology are used properly and prudently, we ourselves must understand science and technology. We must be involved in the decision-making process.

Carl Sagan

OccupyScience? The full essay by Carl Sagan can be found here.

[Daniel] Obligatory vegan story request. What was it that led you to become a vegan? Give us a little background.

[Eric] I gave up meat when I was 17 and went vegan at 18 but it did not last, due to a lack of understanding of basic nutrition and an aversion to vegetables at the time. Over time my palate has changed and I know how to eat after educating myself.

What do you do with your time when you’re not working on Vegan Bodega?

I am a stay at home dad, I photograph now and then, build websites, and cook for my family.

Tell me about the exact moment you realized Vegan Bodega was going to happen.

Well, the thought had been in my mind for a while, and one day I started to talk about my idea with my significant other. I was explaining the market and how NY vegans were waiting for a place like this. She just looked at me and said, ‘It sounds great, do it!”

What inspired you to start Vegan Bodega? Do you have any vegan entrepreneur heroes or mentors?

The inspiration came from two sources – seeing shops in the Pacific Northwest, and a trip to Orlando, my hometown. When I went to Seattle and Portland over two years ago, I saw functioning money making businesses and thought NYC needed one. I didn’t think I could do it until I found Artichoke Red in Florida. This small shop was surviving in a tiny market for vegans and producing positive cash flow. Seeing that store, I knew this was could work. I can’t name everyone I look up to, but so many vegan business owners have been supportive with their guidance.

Looking back at yourself as a child and young adult, could you have foreseen yourself running a food business? What in your life pushed you towards this path?

Having worked in the restaurant industry since my first real employment, I thought it was just a field I would be in as I went through high school and college. Turns out I love food, sharing my favorites and seeing people really enjoying what they are eating.

Your indiegogo.com campaign site doesn’t mention a potential location, but I read in the Village Voice food column that you’re looking at the Lower East Side. What are your thoughts on location and hours? Delivery?

We feel that the store needs to be close to as many different modes of public transportation as possible, as most customers will be traveling 15-30  minutes or more to visit us. The Lower East Side has that, as well as other vegan shops and a great atmosphere. Hours have not yet been determined. Right now, we are working with the idea of 10AM – 8PM six days a week to start and see how folks like those hours and if people need us open more often. Concerning delivery, we are trying to determine how it will work in regards to a minimum order, maximum radius, and delivery fees. Everything depends on what our shoppers want and request.

What do you think people should be most excited about when shopping at Vegan Bodega? Are there particular items that you find people request often? Do you predict any popular items? Any exclusives?

What, you mean an all vegan store isn’t enough to get you so excited you wet yourself? I think some of the more interesting things will be the vintage 70′s candy machine dispensing vegan and accidentally vegan candies for the kids (both big and small,) the prospect of sliced meat substitutes by the pound and getting most everything you need and want in one go. As with any large community, everyone has their own tastes and we haven’t had a lot of repeated requests, save Upton’s Natural seitan. I think some of the more popular items will be candies, Cavi-Art, and some local food producers we are talking to about carrying their products. I don’t think we will have anything exclusive. But I believe, though I could be wrong, that we will be the only store in the Northeast to carry 2 or 3 kinds of vegan queso.

Will Vegan Bodega have a deli counter that makes sandwiches, or will it be by-the-pound? Any surprises in store? (no pun intended)

Currently, we are looking at having the aforementioned sliced meat alternatives but after the store is up and running, we will investigate if the demand is there for sandwiches. We are also looking at having other non-sliced items to weigh and sell. Chick’n salad, raw cole slaw, and some other items.

Will vegan bodega offer cosmetics and accessories from vegan companies? Tell us what a girlie-girl has to look forward to.

Well, that is a great question. We are planning on stocking toiletries and everyday items like lip balm, hair care products, etc. We are extremely interested in hearing what vegans would like us to carry. Although we are going to be heavily focused on food, we want to have what our customers need, within reason.

I hear you’re into vegan fashion. Can you recommend any designers, stores to vegan new yorkers?

Well, I’m more into fashion as a byproduct of working in photography, where I predominately work on fashion and lifestyle shoots. Most of the designers I know are thanks to my significant other being a compendium of vegan info as well as big into supporting new businesses. Leanne Hilgart of Vaute Couture is fantastic and gave us great business advice, then there is Elizabeth Olsen’s Olsen Haus shoes, Julie and Gina of Cri de Coeur, Joshua Katcher’s small runs of eco-concious fashion, Dan Mims and there are loads of others, but they are all well covered in GGA and other NYC blogs. I’m not so hip that I know of small designers on the verge of breaking big.

What’s your favorite vegan product. Favorite vegan restaurant? Favorite vegan meal?

Product right now is Chris and Dan’s creation, Dun-Well Doughnuts. I don’t have one favorite and when my family really likes a place, we eat there all the time until we find a new one. Favorite meal is still probably the Massaman Curry at Pukk.

Why should non-vegans be excited about a vegan convenience store? Do you think that your store will create some awareness?

I think anything new and interesting is both exciting and scary for some. I think it will serve as a great place for people to take their friends when they are curious or say to them, “Wow, you’re vegan, I could never do that. If you don’t eat meat or cheese, what’s left to live for?”, or a variation of that same old question.

Thanks to Eric Hopf for taking time out of a busy schedule to share the inside scoop on his inspiring Vegan Bodega project. At the time of this writing, the Vegan Bodega fund-raising campaign on indiegogo.com had raised $3,230 of the $15,000 goal. To support the Vegan Bodega fund-raising campaign, visit their indiegogo.com page:

http://www.indiegogo.com/Vegan-Bodega-NYCs-Vegan-Convenience-Store

In comparative biology software seems to follow the precedent of predecessors when it comes to data formats. Though XML has been the de facto standard for data marshaling (serialization into a standard format) ubiquitously for many years, it’s only as of the past couple of years that XML has made it into phylogenetics research, in the form of NeXML and PhyloXML.

When I started the project, the first decision I had to deal with was which XML standard to use. Having both a near nil knowledge of both evolutionary biology, and of the new XML standards, I had to lean heavily on my fabulous mentor, James Estill to fill in the gaps and forge ahead with that decision. Jamie had chosen NeXML for it’s flat structure, whereas PhyloXML had a more traditional nested structure that didn’t seem to lend itself to straightforward processing and readability. NeXML also offers referencing an ontology via namespaces, and has robust perl library support in Bio::Phylo and BioPerl. The authors of both XML standards are involved in working groups at NESCent, where we all work, so we’d have great access to support either way.

Jamie set up a initial wiki page for our new NeXML template, and after some discussions with standard author and Bio::Phylo lead Rutger Vos, we settled on a final template form. This form puts reconciliation info about trees in the top level Trees element, and the mappings of guest nodes onto host nodes or edges are attached to the guest nodes. All information is does with meta tags, which Bio::Phylo can extract handily. That takes of the the XML side of things, and the amount of code needed for parsing seems to back up the argument that a flat mapping is simpler to handle than a nested one. Parsing is done using Bio::Phylo which has stronger NeXML support than plain BioPerl.

With the XML side mostly wrapped up, the question of legacy formats comes next. NHX (and variants) was, before XML came around, a popular way to serialize richly annotated trees, for lack of better options. Variations like PRIME were created to support extra attributes (like duplication events) that weren’t supported by plain Newick (NHX). Two of the three software packages (PrimeGSR/TV and TreeBest) use this NHX variant, and so it’s important to, for the foreseeable future, support input and output for NHX variants. The best way to do this, is to build on existing NHX support in BioPerl. Jamie had done some processing on PRIME, but that code isn’t easy to desirable to maintain, so a more standard approach would be preferred for ongoing support.

With XML and NHX IO taken care of, the next issue is working with the existing iPlant database, which has been populated via Jamie’s PRIME parsing code and TreeBest PRIME output with 2500 gene family mappings to 6 plant species. I have the original 2500 PRIME output files, and access to the database, so I there is enough data to compare a new parsing method to the original method employed for the initial import.

If the module were to be only used for direct IO, then the internal object wouldn’t matter very much. The tree could be a generic no nonsense linked list structure, or it could be an augmented BioPerl or Bio::Phylo::Forest::Tree object, with all the accoutrements. However, there is a final concern, which is use of the new perl object in the iplant infrastructure. The only use case for this type of use so far is the tree viewer, a Java web application which renders the trees and uses the iPlant TR database to decorate the trees to indicate relationships and mappings. I am planning to speak with one of the Java developers today to get a better sense of how if at all my code might be helpful this summer. It is possible that the existing JSON support in the TR database backend written my Jamie would better support the Java viewer in the short term.

Ahead of my call today with Todd Vision and Jamie, some important questions are:

• Will the new parser be used strictly for IO
• What are the use cases and requirements for anything beyond simple IO
• Therefore, what specific architecture requirements would there be for the perl object? (based on viewer requirements, or other potential use cases)

My intuition is that simple IO is the primary objective for this summer, but I am keeping an open mind. One area where the Java viewer might benefit from the new code is to be able to load reconciliations directly from NHX or NeXML files, rather than requiring a fully functional TR backend and database (Naim mentioned this).

Use cases for simple IO are:

• Load NeXML and NHX based reconciliations into the database
• Output NeXML reconciliations from the database

There are a number of things that the perl parser module might supply to a user, if use cases supported the need:

• Individual reconciliations and trees requested by ID/species/gene name
• Cursor based retrieval of records from a large set of mappings
• Support deep hierarchical access to the trees and mappings (as in standard complex tree objects)

The parser is in early stages, and so far I have looked at parsing NeXML and NHX, but haven’t started on iplant database support yet, as this is somewhat tied into the viewer problem, since existing database retrieval code is for that purpose/use. My next objective, if simple IO is the priority, is to release a version that supports NeXML fully, and then NHX, and then iPlant DB, but not necessarily in that order. Demonstrating use of this code would be to go between TreeBest output and NeXML output, for example, as mentioned above.

The basic idea of our proposal, is to introduce an element into the NeXML schema that encapsulates mappings between species (host) tree edges, and gene (guest) tree nodes. This allows for gene duplication and speciation events, and potentially horizontal gene transfer and other events as defined by some ontology. Mapped edges defined with the same node endpoint represent a speciation, while edges defined by two nodes represent a duplication. Using only just node could indicate horizontal transfer.

You can find the proposal here. Please post a comment on my blog or email me if you happen to be in evolutionary biology and have thoughts about GTR!

Since tree reconciliation is a phylogenetic technique that affects many researchers, tools, and platforms, our next goal is to obtain feedback from the NeXML maintainer, Rutger Vos, the PhyloXML maintainer, Chris Zmasek (both of whom have participated in the evoinfo working group at NESCent), my other GSOC mentors, and the larger research community at NESCent and beyond. Once we know we’re on the right path, have a plan to get developers on board, and have a functional open source proof of concept via the iPlant platform and BioPerl, we’ll be able to consider the project successful.

My focus this week is on figuring out BioPerl/Bio::Phylo tree functionality to identify which parser/library to focus on when implementing the new XML support. There’s also the question of how the schema will be updated, or if NexML is ultimately even the best technology to build on. Thankfully I have direct access to those who maintain phyloinformatics standards via NESCent.

Beyond the immediate XML implementation needs, I’m also, as time permits, looking at the iplant tree reconciliation schema and the import scripts that work on data from the pipeline. I’ll be looking at primeGSR and TreeBeST, and getting a basic understanding of their reconciliation features. I’ve had to do a bit of molecular biology and genetics review in order to keep up, which is great, because I’m going to be neck-deep in this stuff once classes start, so I’ve got a great head start.