Those who have been watching may have noticed I quietly started developing an Android application in the last month or so. It’s still super-buggy and far from feature complete, but I thought it was time to announce it here (”release early, release often”). It’s not ready for real users yet, but developers may like to take a little look.

Occyd (-k d .. sounds like rockied or oggied) is an application for tagging geolocations, aimed at GPS-enabled network-connected devices. It currently consists of an Android client, and a server backend running on Google App Engine. The (evolving) API is simple enough that it should be easy to write clients (or servers) for various platforms. The idea is to enable people to tag locations on the surface of the planet with a list of keywords, just like they can tag web pages with delicious. They should also be able to search for tagged locations, based on tag(s), on distance from their current location and recency of the post.

Here’s one possible elevator pitch (for a very long, slow elevator ride):

“You are a member of a large bird watching club. Your members like to record where they have spotted various species, and use Occyd to share the locations at which they have sighted various birds. You are out in the park, when you spot the rare Orange Bellied Parrot. You pull out your Android phone, fire up the Occyd client which automatically knows your location via GPS, and tag that current location ‘orangebelliedparrot parrot birds’. You then decide to see if others have spotted parrots in the area. You search for ‘parrot’ in the Occyd client; a map appears showing the locations of all the other sightings tagged ‘parrot’ in your vacinity. You tweak the search settings to show only ‘parrot’ sightings within 100 metres and 14 days … on the map you see that your friend RobHill spotted an Orange Bellied Parrot here last week – looks like the numbers of this population are recovering !”

Ponder for a bit, and I’m sure you can think up at least a handful of other great uses (tagging good fishing spots, favorite cafes, or maybe even sightings of parking inspectors ).

As with any new project, there are lots more ideas than time to implement them (and I have a day job that doesn’t involve Occyd …). The Occyd Android client and Occyd GAE server source is currently available under the GPL v3 on GitHub, and I’m keeping all my documentation and notes on the Occyd Android client wiki provided at GitHub. Watch this space ….

I’ve found QR-code “2D barcodes” really handy when playing with my Android phone.

Sometimes, I have a web page open on my desktop PC, and I want to quickly load it in the Android Chrome browser to see what it looks like. Rather than re-typing it with my thumbs, the Barcode Scanner application allows me to scan a QR-code from the screen of my computer, and if the decoded text contains a URL, open it in the Android browser.

These two bookmarklets turn the URL of the current page that is open in your browser into a scannable QR-code:

Google Charts API based bookmarklet: Drag this link –>Current URL to QR-code to your bookmarks toolbar.

The code is:
javascript:location.href='http://chart.apis.google.com/chart?cht=qr&chs=350x350&chl='+escape(location.href);

Alternatively, I made a Kaywa QR-code generator version. Drag this link –>Current URL to QR-code to your bookmarks toolbar.

The code is:
javascript:location.href='http://qrcode.kaywa.com/img.php?s=8&d='+escape(location.href);

They both do the same thing, so you probably only want one. Only tested on Firefox.

(Update:  seemed Wordpress ate the javascript in the bookmarklet links … should be okay now)

Essentially, this seems to be: add the tag ‘geotagged‘, along with the tags ‘geo:lat=X.xxx‘ and ‘geo:lon=X.xxx‘, where the X.xxx’s are the latitude and longtitude numbers that are likely to come straight out of your GPS, in decimal degrees (WGS84).

This is all very nice, but the problem with tags in this format is that there is no easy or efficient way to use them to retrieve all items tagged for a particular locality. Sure, if I’m standing right on top of the Eureka Tower at -37.821362,144.964213, I can search for tags geo:lat=-37.821362 and geo:lon=144.964213 to find all the geotagged links for that exact location, but what if I’m standing 50 metres across the street looking up at the tower and want to search for links near my current location ?

Enter the geohash, a hash function for geolocation coordinates invented by Gustavo Niemeyer (not to be confused with the xkcd Spontaneous Adventure Generation algorithm of the same name). Wikipedia gives a reasonable explanation of how geohashes work … essentially the latitude and longitude are encoded as strings like r1r0fdzdwg. Geohashes have the useful property of having arbitrary precision … geohashes with the same prefix represent locations in the same vicinity. This means that the location across the street from the Eureka tower, at geohash r1r0fdy7sm, shares the prefix r1r0fd with the geohash closest to the top of the Eureka Tower, at r1r0fdzdwg.

My proposal for delicious geotaggers is that in addition to the geo:lat and geo:lon tags, several truncated geo:hash tags should also be used. If I were to bookmark something related to the Eureka Tower, I may tag it:

geotagged
geo:lat=-37.821362
geo:lon=144.964213
geo:hash=r1r0fdzdwg
geo:hash=r1r0fdz
geo:hash=r1r0f

Then, anyone searching for the tag geo:hash=r1r0f will find every item within the area that this geohash covers … this would include not only the Eureka Tower, but the Rialto Towers too.

For each bookmarked item, the number of truncated geohashes used as tags roughly determine the distance ranges (ie bounding boxes) that can be searched. Exactly which truncations, or how many geohash tags to use, is an existing problem that I haven’t yet decided the best solution for; is it best to ‘overload’ with every possible geohash truncation (eg include tags geo:hash=r1r0fdzdwg, geo:hash=r1r0fdzdwg, geo:hash=r1r0fdzdw, geo:hash=r1r0fdzd, geo:hash=r1r0fdz …etc… to geo:hash=r) ? This is probably overkill. A better approach would be to choose just a few key truncations that roughly correlate to a range of sensibly sized patches on the Earths surface, eg, bounding boxes with diagonal lengths of:

• geo:hash=r1r0fdzdwg ~60 cm ['exact']
• geo:hash=r1r0fdzd ~20 m
• geo:hash=r1r0fdz ~150 m
• geo:hash=r1r0fd ~600 m
• geo:hash=r1r0f ~4.8 km
• geo:hash=r1r0 ~19.5 km
• geo:hash=r1r ~150 km

These ranges map loosely to those deemed useful by Brightkite, which lets you search for events around you within 20 m, 200 m, 2 km, 4 km, 10 km, 50 km and 100 km. Maybe we only need a few of these. If only a few truncations were provided by the tagger, the user can always execute multiple searches, starting from the full geohash of their current location and truncating back, character by character, (effectively expanding the search radius) until they start to get hits. There may also be techniques whereby the last character(s) of the truncated hash can be incremented/decremented to search neighboring bounding boxes (eg for r1r0fd, also search for r1r0fc, r1r0fe tags), although I need to think about this a little more.

Of course, the best solution for more useful geotagging within delicious would be for delicious/Yahoo to explicitly support some style of geotagging and provide a geotag-aware search facility … but until that day, geohashes may well do the job well enough. Next step for me: write a proof of concept application that actually produces and makes use of these types of tags ….

I think comfort with meaninglessness is an important skill in studying biology (and probably other sciences too). Many times, during the description of a system, various acronyms are thrown about as labels for entities (or ‘actors’) in that system. An important skill of the scientist is being able to follow how all the actors in the system relate to each other, without necessarily knowing anything about the specific properties of those actors. There are lots of protein and gene names which often bear very little meaning relative to the biological entity that they label, and fixating on what ‘the name’ means simply distracts from the true nature of the entity.

Example: TPR proteins are a superfamily of protein fold, often involved in protein-protein interactions. I have sometimes been asked at poster presentations, or the occasional talk: “What does TPR stand for ?”. “TPR” is an acronym for “tetratricopeptide repeat” … you may be able to glean from that expansion that the protein fold is composed of repeat sequences 34 amino acids long – but that is only one small aspect of the family, and isn’t the important point. Yet many molecular biologists appear uncomfortable with an “undefined” acronym, and insist on having it expanded to reveal the full name. TPR is just a convenient label for the superfamily … it could equally have been called GrratBlat or 5450520A, it would still be the same thing. The point is, you shouldn’t have to ask what TPR stands for. Sure, it’s a curiosity, and some protein names can be amusing (Sonic Hedgehog, or “Just Another Kinase” come to mind), it may also contain some meaning, but first and foremost it’s a label – something to link the entity to all the other descriptive information about it’s structure, function, localisation and regulation. Like many classes of protein, the original name was given at a time when little was actually known about the thing, and typically the meaning embedded in the name should be ignored lest it bias our interpretation about what that protein really does.

Summary of opinion: Molecular biologists should become comfortable with the notion that a name is just a label – meaningless without the associated metadata.

All of this is probably second nature those who studied philosophy (or computer science, or linguistics) … I’m guessing it is an issue of semantics. I really should have taken some of those subjects back in my undergrad days …

1. What is your blog about?

I often ask myself this question. Being a scientist, I always feel like it should be about science, and the various biological systems I work with. I reality, it is about programming, bioinformatics, the web with the tiniest bit of structural biology thrown in. I used to blog about Linux related things occasionally, but I split that off into another blog (which gets 10 times more traffic ).

2. What will you never write about?

I’d rather not rule anything out. I’ve avoided politics, largely because all my “blogging peers” also largely avoid it. Sometime I wonder why, but I think I’m beginning to understand; blogging about political issues may seem important, but eventually it just becomes a constant ‘rah rah rah‘. That would get boring. So I’m saving it for when it really matters (the proposed ‘filtering’ of internet connections at the ISP level by the Australian government is coming close. There, I did it ).

3. Have you ever considered leaving science?

Yes. But I did cheat and read Bora’s answer to this one (by accident).
I think it would be impossible to leave ’science’ unless I became permanently brain damaged or something. Leave research … sure, it crosses my mind from time to time.

4. What would you do instead?

I’d try my best to get a job in video game development, or web application development (or both … developing a web-based game !). I’d try to work my experience as a scientist into this endeavour. Not sure how successful I would be, but I’m trying to slowly build up a portfolio, just in case

5. What do you think will science blogging be like in 5 years?

I think research groups will be tied together more and more by their blogs. A bit like the way RRRosie Redfield runs things. Not necessarily blanket Open Notebook Science (give it 10 years), but certainly a greater level of open, public communication of ideas.

6. What is the most extraordinary thing that happened to you because of blogging?

It’s not that exciting, but it’s the best I’ve got; I was contacted by an real journalist with some questions about the role of cloud computing for academic research. I didn’t really feel qualified to comment a length, since it largely stemmed from a ‘what if’ type idea I blogged about. But I gave my perspective anyhow.

7. Did you write a blog post or comment you later regretted?

Yes, quite often. I have a tendancy to always be in a hurry when commenting, coupled with a desire to not be overly self-censoring. I’m never trying to sound like a kook, troll or A-hole … it just turns out that way sometimes. Personally I find it takes a long time to write a concise, clear comment, beyond “LOL”. The FriendFeed comment box is always too small for me, but that’s a good thing, since it forces me to summarise.

8. When did you first learn about science blogging?

Not exactly sure, but I think it was via nodalpoint.org the bioinformatics weblog. I wrote one or two posts for nodalpoint. Around the time I was writing my PhD thesis, a few netziens of nodalpoint started blogs (or I discovered that they had blogs outside of nodalpoint). The most influential for me were Neil Saunders’ “What You’re Doing is Rather Desparate”, and well as Pedro Beltrao’s “Public Rambling” and Duncan Hull’s “O’Really ?”. I thought, “I can do that”, so I started a Blogger blog. One year later I moved to a self-hosted Wordpress blog. But lets not get side tracked with a boring meta-discussion about blogging software.

9. What do your colleagues at work say about your blogging?

Mostly, they are unaware. Occasionally I have dropped a comment about “my blog”, but no one has really jumped on it. Which is fine, since I don’t really blog about anything that most of them have any interest in.

Well, that’s it. Now to read everyone else’s responses ……

(Originally via Blog Around the Clock [Bora Zivkovic], via FriendFeed)

For example, typing:

gg open science on friendfeed

into the YubNub search box searches Google for “open science on friendfeed“, via YubNub.

I thought I’d highlight a few life science- and bioinformatics-related YubNub commands I find myself using quite often in my day-to-day work. Some are commands I created, others someone else created. This is the beauty of YubNub … often someone has already made the ‘obvious’ command … it’s worth just trying to search with a command you expect to exist, since it often does.

Onward, with the list:

• pubmed — Searches PubMed
• hubmed — Searches HubMed (Alf Eatons featureful alternative interface to PubMed)
• gopubmed — Searches GoPubMed (an ontology enhanced PubMed search)
• doi — Redirects you based on a Digital Object Identifier (DOI), via http://dx.doi.org/
• pdb — Searches the Protein DataBank for 3D structures. Usually the search term should be a 4 letter pdb code.
• uniprot — Searches the Uniprot database (use an accession, id or keyword as the query).
• ihop — Searches iHOP, information Hyperlinked over Proteins, for views of the biomedical literature guided by gene networks. Nothing to do with pancakes (or prayer).

There is also a class of more general, non-biomedical commands which I often use:

• gg — The Google.
• gim — The Google Image Search.
• wp — Good ol’ Wikipedia.
• ucc – The universal currency converter at XE.com. Use it like ucc 399 aud usd, to convert $399 Australian dollars to US dollars. Then, if you have your cash in Australian dollars, weep about the recent drop in the exchange rate
• man — Like *nix man ‘manual pages’, but for YubNub commands. Eg, man ucc will give the manual page describing how to used the ucc command.
• ls — A bit like the *nix shell ls, this command lists existing YubNub commands that contain your query in their name, description or url. eg. searching ls protein gives you a short list of all the commands related to proteins.

I’ve installed the YubNub opensearch plugin so I can search directly from the search box (or location bar) in Firefox. Maybe one day Ubiquity will fulfill this purpose, since in many way it is the natural progression of the YubNub idea. But for the moment YubNub is the fastest, most streamlined way I’ve found to quickly fire off a search when I need to hunt down a reference, protein sequence or 3D structure. Nothing like instant gratification

Around three weeks ago I attended the Synthetic Biology 4.0 meeting in Hong Kong, hosted by the Hong Kong University of Science and Technology. I’ve taken a little time to allow all the new and exciting ideas to sink in. I really enjoyed the meeting, and while it was a little short it was an effective way to quickly sample the current developments in synthetic biology, as it stands.

Some highlights

Here are some summaries on a few highlight presentations. Due to parallel sessions, I couldn’t see every talk; luckily I’ll be able to catch up on those I missed once the videos appear online.

Clyde Hutchison (J. Craig Venter Institute), spoke about genome construction, specifically about rebuilding the minimal genome on Mycoplasma genitalium by synthesis of large fragments and subsequent stepwise assembly. This is probably not brand new work, but it was the first time I’d seen it presented. Turns out they could fully assemble the genome into a yeast vector from 25 large fragments using a ’shot-gun’ approach with subsequent PCR screening to identify the correctly assembled construct.

Christopher Voight (UCSF) (and a poster presentation by Travis Bayer et al): Bio-MeX: A Novel Route from Biomass to Gasoline and Petrochemicals. Chris spoke about the work his lab is doing on producing methyl halides in E. coli and yeast. Methyl halides are a common feedstock in the petrochemical industry for producing many other organic chemicals, so a non-fossil fuel source will be useful in the future. I’ve always been a little skeptical about ocean metagenomic studies that sell themselves as the solution to the worlds energy problems, based on the notion that an amazing new enzyme will be discovered in marine bacteria. Well, this work coming out of Chris’ lab could prove me wrong … after screening 89 putative homologs of a methyl halide transferases from the various kingdoms of life (most annotated ‘methyl transferase’ in sequence database), the best one turned out the be from an “uncultured marine bacteria”, discovered by the Sargasso Sea Sequencing Project.

Eric Winfree (CalTech) spoke about his experiments with DNA tile-based crystals, as a potential model system for pre-biotic life. Crystal growth, breakage and regrowth models replication, the tiled ‘layers’ of different crystal variants form the genome. Don’t be mislead and assume that Eric is proposing that DNA of this nature was actually around in the primordial soup … it’s simply being used as a well understood system enabling specific molecular complementarity and template based replication (with errors); in theory this type of system could be built using any ‘crystal’ with similar properties.

Jay Keasling (UC Berkley, LBNL): Fuel and Drug Production: Jay gave some facts and figures about biofuel production from the metabolically engineered organisms which are ultimately being commercialised at Amyris. It was noted in the opening slides of several talks at this conference: Ethanol is not considered a very good gasoline replacement (lower energy density, too hydroscopic for existing pipeline infrastructure, high octane rating) when compared with n-butanol (higher energy density, less hydroscopic, controlled volitility, similar octane rating to gasoline). Watch the video for some well handled but potentially hairy questions about the source of feedstocks for biofuels production. On the science-side, Jay showed some interesting results from studies testing the effect of scaffolds for co-localising enzymes in a biosynthetic pathway of interest (as fusion proteins to PDZ, SH3 etc domains). After screening a library of scaffolds that would arrange different numbers of enzymes in different orders, one specific arrangment (”A-B-B-C-C”) worked better than other variations. No rational explaination, but interesting nonetheless.

Patrick Boyle et al from Pamela Silvers lab:  (poster presentation, The Synthetic Hydrogenosome: Subcellular Engineering for Biohydrogen production): showed how he was engineering yeast mitochondria for hydrogen production by introducing components of the pathway responsible from hydrogenosomes. This work caught my interest since for the past few years I’ve worked on aspects of protein import into mitochondria and related organelles (including a little bit of collaborative work on hydrogenosomes recently). Early versions of the engineered strain were producing small amounts of hydrogen compared with wildtype yeast … it will be interesting to see how far this can be optimized in the future (I don’t expect it to fuel a hydrogen economy anytime soon, but it’s early days).

Priscilla Purnick (Yale) spoke about her work helping engineer embryonic stem cells with genetic circuits to precisely control proliferation, differentiation and cell death, with the ultimate goal of treating Type I Diabetes with self-regulating beta-like insulin secreting cells. I couldn’t do justice to the technical details in a short summary here, needless to say it’s complex and impressive looking work. This was a spin off project from the Princeton iGEM team using many ‘off the shelf’ BioBricks(tm). While still in the early stages, the talk showed a nice mix of systems biology style modeling and hard experimental data.

I sat in on an open discussion session, entitled Legal Schemes and Rights. The key point that surprised me here was how little had actually been figured out surrounding the ‘intellectual property’ law of sharing, modifying, combining and (potentially) commercializing individual BioBrick[tm]-style parts, and devices built with such parts. I’d been under the delusion that the legal side was figured out early on, and that BioBrick parts were shared under some sort of MIT-like or BSD-like license. This is apparently not the case. Various possible legal frameworks were outlined, but I think the most insightful advice I heard was something to the effect of (paraphrased) .. “Don’t sit around treating this like an interesting academic problem .. pretty soon (~12 months ?) community norms for licensing parts will emerge by necessity and under the force of commercial interests, not by careful or considered design, and if you haven’t worked to establish things in the way that is best for proliferation of the technology and all stakeholders, it will be too late to change course. We have seen this has happen in other industries, it will happen here too”. Watch the videos once they appear if you want the correct quote, I can’t remember who said it now

I’ve half written a “part 2″ to this post, outlining some ideas on the current state of Synthetic Biology as a field … but I’ll probably never publish it since it’s mostly just me organizing my slightly opinionated thoughts out loud. The summary is: there is currently a lot of excitement, potentially a little hype (see Gartner’s hype cycle, pick where you think Synthetic Biology currently sits on the curve). It will be interesting how this pans out, particularly if expectations have been unrealistically inflated. There has also been a bit of quibbling over the definition of Synthetic Biology; those engineers that have forged the field are probably pretty bored of the old ‘definition debate’ by now, but many biologists still don’t really know what Synthetic Biology is. Based on discussions I’ve had with colleagues about the conference content upon returning, the average molecular biologist doesn’t always see how Synthetic Biology is very different to what various bioscientists have been doing under the banner of Biotechnology for many years. My simplest explaination is that the underlying technologies are essentially the same, but the approach, the application of formal engineering principles and their use in a rational way to create useful ‘devices’, is different from past practices that have largely focused on discovering new knowledge about biological systems with many useful technologies arising in a more ‘undirected’ and opportunistic fashion. It’s great to be living in a time when the foundational knowledge in biology, built on decades (centuries?) of basic research, are slowly beginning to come to fruition in rationally designed technologies.

For another perspective, and little more on the buzz outside of the formal presentations, see Jonathan Clines “Word on the Street @ SB 4.0″ posts.

It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol.

Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check.

(oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye).

Couldn’t help myself … everyone else is doing it

Recently I needed to install NCBI wwwblast on my local workstation to enable some software that needed to interface with BLAST via the web service. It was straightforward to install, but I took some notes, because there were a few changes required with respect to the official wwwblast documentation at NCBI. These instructions are for Ubuntu 8.04, but probably will work with many recent flavours of Debian.

Download and install

Download NCBI wwwblast from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/ (The version I used was wwwblast-2.2.18-ia32-linux.tar.gz).

Untar it into /var/www/ , preserving permissions.

$ cd /var/www/

$ sudo tar zxvpf wwwblast-2.2.18-ia32-linux.tar.gz

You will also need to make sure csh (the “C-shell”) is installed, since the blast.cgi script needs this to run:

$ sudo apt-get install csh

(Thanks to jpopesku for spotting this missing package [comments below])

Set up Apache2

The instructions in the official wwwblast manual didn’t seem to work for Apache2 .. (could be a typo: Follow SymLinks should be FollowSymLinks … one camel-case word without the space). I put this in into the VirtualHost definition in the standard /etc/apache2/sites-available/default file used by Apache2 in Ubuntu 8.04.

The code above was inserted just before the </VirtualHost> closing tag.

Restart Apache for good measure.

$ sudo /etc/init.d/apache2 restart

Configure your wwwblast to see your databases

Assuming you already have some existing BLAST formatted databases made with formatdb, you will then need to configure wwwblast to find them, as per the manual. In short, this involves putting the BLAST database files into /var/www/blast/db/ (or symlinking to the files), modifying /var/www/blast/blast.rc (or one of the other *.rc files, for other BLAST programs, eg psiblast) to associate the database name with a BLAST program, and modifying the dropdown database list in /var/www/blast/blast.html (or one of the other *.html files for other BLAST programs) to add the name of the database(s).

My BLAST databases live in /data/databases/blast/, so I simply moved the example database directory /var/www/blast/db to /var/www/blast/db.orig:

$ sudo mv  /var/www/blast/db /var/www/blast/db.orig

then symlinked /var/www/blast/db to /data/databases/blast:

$ sudo ln -s /data/databases/blast /var/www/blast/db

In /var/www/blast/blast.rc I changed the line:

blastp test_aa_db

to:

blastp nr swissprot pdbaa

(you may also want to configure blastn etc in the same way)

In /var/www/blast/blast.html, I changed the test database code:

to:

(you may want to do this for other BLAST programs too, eg also edit psiblast.html)

This will allow be to search the nr, swissprot and pdbaa databases I have installed using plain-vanilla BLAST.

Test it out

Go to http://localhost/blast/blast.html.

You should find the wwwblast interface, with a dropdown box featuring the database(s) you added. Run a test search with your favorite sequences (ensure you also select the correct blast program, eg blastp !). Enjoy using your own CPU time !