Category Archives: Research

Photography is not a hobby. Updated CV and feedback request.

Visual resumeYesterday I asked over at FriendFeed for the feedback on my early attempt of making visual CV (big thanks to all who commented). Here’s a revised version that hopefully looks much better. The key to read the image above (click to see larger version) is as follows: Y-axis represents time (with dotted line indicating more or less the present moment); areas of interest are along X-axis; color of the phrases indicates my confidence level; font size denotes amount of time I spent on the topic (so in this case I have spent lots of time using perl, but I still don’t feel very confident about it); placement of the phrases denotes which areas of interest particular project/phrase spans; area below the dotted line shows my approximate plans and hopes for the future.

The first version had “Photography” area instead of “Visualization”, but I needed to change that since it was confusing everybody and raised questions why I put a hobby on a professional CV. Photography (or visual arts) is not my hobby. My hobby is choir singing (which I do for over 14 years already, currently singing jazz and gospel). Visualization/Photography is there to indicate that I consider data visualization one of the most important elements of scientific method. What I’m trying to figure out is what kind of presentation can help us in understanding really complex systems, such as human (genetic, to make it easier) diseases. And when we understand them curing is going to be much easier. At least I hope it will.

Anyway, the true reason to post it is to ask my readers for feedback on missing elements of my plans. So far my ideas for the future research projects split into a few paths. First path is to work further on bacterial systems (or subsystems, such as secretion systems etc.). This work would translate later on into something I call Synthetic Biology Framework, which would be a tool helping in designing new biological systems, and maybe later would result in creating a programming language for a cell. My first ideas about the framework were to design engineered bacteria producing some important compounds, maybe drugs, but now I think the cooler use for the framework would be to design bionano machines. The second path is about modelling of human diseases, with important milestone which is analysis of human genome and metagenome (genobiome as I call it) – if the data will be available. Because I don’t think I could do better here than thousands of scientists if I were using the same information, here’s a moment where synthetic biology comes into play again – I hope that I could design nanomachines that would server as quick diagnostic tools or would be reporting the body state in some mostly non-invasive way (aiming at issue of “how is my cholesterol level building up”). The third path is mostly empty and concerns visualization methods. So far I have no clear idea how to build a system that would visually assist in understanding how cells work. I plan to experiment with 3D printing and 3D visualization of biological networks, but I have no clear idea where this will lead me.

So if you have some opinion, comment, idea how to connect some dots, how to jump from one area to another (for example I have no yet idea how to approach pharmacogenomics), or if you think that it doesn’t make sense at all feel free to comment.

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Posted by on November 18, 2008 in Career, Research


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Thinking about RaaS: Research-as-a-Service

The research li...

Image by Getty Images via Daylife

Instead of disclaimer: this is a bunch of loose thoughts on an element of a possible future of research. I’m only touching some issues here and still I don’t have coherent vision of the commercial side of research. So, feel free to show me I’m very wrong – you’ll save me lots of time of coming to your conclusions :).

According to Wikipedia, Everything as a Service is a:

concept of being able to call up re-usable, fine-grained software components across a network.

While the most common example is SaaS – Software as a Service, this concept can be applied to other functions such as communication, infrastructure or data (the last one sounds very interesting). It recently occurred to me, that investments (or maybe I should call these partnerships) of biotech and pharma companies in academic research institutions are good examples of RaaS, Research as a Service. I think every situation where the research is done after the agreement (buying or licensing patented innovation doesn’t qualify) can be called RaaS.


To a company, there are obvious advantages of hiring scientists to get the research done, but I think there also would be plenty of good sides of such arrangement for us (of course I have no experience yet). Probably the biggest plus would be money and ability to get them in somehow predictable manner. I think it’s also important to be stretched intellectually from time to time (I assume that easy things aren’t worth outsourcing).

Many flavors of RaaS

Paying to an academic institution to come up with a new drug candidate is only one of many types of RaaS. There’s researching a given problem (something Innocentive or Nine Sigma are coordinating), coming up with an innovation (drug candidate example), providing expertise (consulting) or innovating and delivering (designing, building and implementing new machine, workflow or pipeline). We could find examples of all types happening everyday, but probably not in all scientific fields. Delivering something in biology is usually quite expensive and time consuming, while consulting gigs in quantum physics don’t appear all that often.

The point is that all these RaaS flavors can and are applied to academic institutions. In other words, many researchers provide commercial services using time and equipment paid from taxpayers money. And I think it’s not an issue – even more: it should be finally admitted and accepted (so we could get rid of the artificial division of researches into academic and all others; but that’s another story), and organized, so we could provide such services easier and more often.

Resources all over the place

The Health Commons project aims at building a framework that could help in sharing and organising research process aiming at developing new drugs. We seem to have lots of elements of such environment in place – we have many (or even too many 😉 ) scientists, some service providers, data centers and some work done on standards of operations and information exchange. If we forget about drug development, not much actually changes. We have workforce, some services aimed at researchers and lots of tools that help in communication in both directions.

Here’s example of research scenario: if I were to market a genetic test that identifies mutations resulting in oversensitivity or resistance to a drug (something which I believe will be the next hit after screening for disease markers), the whole research part wouldn’t require any significant involvement from my side. CRO (contract research organization) would take care of identifying patients with specific conditions, sequencing company would get me their genomes (currently $5000 each, but the price is dropping very fast) and as far as I know bioinformatics community, finding people to analyze the data wouldn’t be an issue at all. While such scenario is a bit too optimistic (I skipped lawyers in the process), we already have resources to make it happen.

Where is it going?

I imagine future RaaS provider as a small company (I’m not yet sure if a non-profit organization is a better fit for people interested in doing research; also, I don’t know how fast the issue of academic-commercial blur can be solved) made by a few scientists from different but closely related fields. The reason I see it small, is about mobility. And I don’t mean here physical mobility (which BTW may be required on some occasions) but mobility of focus – the main advantage of small organizations.

I imagine such company would be able to do consulting (and data analysis, maybe on the RedMonk model) and innovate at a software level. It would be able to do the work on site (small group again) and deliver the results quick (“bursty work”).

Pieces of this vision come from old Deepak’s posts and many FriendFeed discussions. I actually think about putting it into practice. What do you think I am missing here (other than marketing 😉 )?

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Posted by on November 3, 2008 in Comments, Research


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Open Access Day

Today is the world’s first Open Access Day . It aims at broadening awareness and understanding of OA. The approach is to make as many people as possible to blog today on the topic, possibly answering the following questions:

  • Why does Open Access matter to you?

In my case, where pretty soon I’ll have no support from a large institution, Open Access means ability to do research. OA is a vital help to small or underfunded research groups.

  • How did you first become aware of it?

Internal policy of my former employer required that all results should be published in OA journals. BTW, it didn’t change since then.

  • Why should scientific and medical research be an open-access resource for the world?

Ability to do research and to innovate shouldn’t be inhibited by access to knowledge and data produced by publicly funded research institutions.

  • What do you do to support Open Access, and what can others do?

I do publish in OA journals (four out of five publications I have so far are OA).

See more OA Day entries at FriendFeed Open Access Day room.

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Posted by on October 14, 2008 in Community, Research


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Many Eyes and literature summary

I’m not the first one to come up with this idea – Ntino posted about it before. However, I didn’t really understand before how powerful it could be. Using Many Eyes visualization capabilities I’ve created a quick browsable summary of abstracts related to a particular protein. I took all abstracts PubMed returned for a particular query (in this case it was “YadA Yersinia”; YadA is a prominent adhesin and important pathogenicity factor in Yersiniae) and uploaded them as text into Many Eyes. I chose “Word Tree” representation and searched for “yada”, which gave a nice graph of the most prominent phases related to this protein/gene name. Maybe it’s not a breakthrough, but compared to the classification/semantification provided by GoPubMed, such approach works much better for entities that aren’t well described in biological ontologies.

Given that the whole concept is pretty straightforward, it would be nice if one of alternative PubMed search engines provided a similar method of summarizing user’s query, don’t you think?

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Posted by on October 4, 2008 in Papers, Research, Visualization


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Future of Science on the (ZuiPrezi) map

I’ve just stumbled across map of predictions about global science and innovation created at a recent IFTF workshop in Singapore (the interface is a novel service for online presentation called ZuiPrezi – it looks very promising and I’m waiting for it to come out of private beta). The map contains a few points that resonate with my own scientific interests:

  • bioelectricity, microbial fuel cells and self-assembly for molecular electronics were for me areas where synthetic biology comes into play
  • scientific publications changing from journals to articles and proposal to make an institute for free exchange of ideas looked like indications that Science 2.0 memes are spreading very well
  • and finally, I’m happy to see more people believing that real-time, non-invasive and possibly 3D sensing of biological processes (aka “how is my cholesterol level building up?”) will be available sooner than in 50 years

As usuall with such predictions, I feel like many of them are quite conservative – or even schematic. Only very few were completely new to me, but that’s not necessarily a bad thing. It means that actually most of these predictions will turn out to be true in some time. I would like to see something that would immediately blow me away, but on the other hand it’s all relative :).

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Posted by on September 30, 2008 in Comments, Research


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How far one can push online collaboration in research?

History comparison reports highlight the chang...Image via Wikipedia

A week or so ago I’ve asked on the FriendFeed if there’s an interest in writing a cyclic publication on the status of Science 2.0. I thought that summarizing every year advancements in openness of science would be a good idea. During discussion it turned out that there’s a need to write a first major publication on Science 2.0 concepts because there isn’t one published in the life sciences field. The final conclusion of interested people was to meet face to face on the upcoming conference and discuss things in detail.

And this made me think.

I started to wonder why people who live, breathe and do research online still need to meet in person to plan and discuss some stuff. The very obvious explanation is that the conference was only two weeks ahead, so there was nothing more than that, but some patterns (brainstorm online, then meet in person, then finish online) repeat so often that I started to believe an online collaboration can only go to a certain point.

The excuse is not in the tools, especially given how fast the new ones appear.  As an examples may serve recently launched Adobe Acrobat site, which contains online editor and live collaboration suite (contains screen sharing, notes, chat, audio, video) or its analog for programmers: Assembla (svn, git, trac, wiki, milestones).

My feeling is that what makes a difference is not a quality of interaction while working on a certain project, but the possibility of discussing things not directly related to this project. Online collaboration is usually very focused. When editing a document online it’s usually hard to side-track it, so at the end it’s about something else than it was planned. Calls or videoconferences have usually a schedule. No place for non-related stuff. No place for a beer/coffee/glass of water and a chat about how life was good in old times. No place for discussions on random things and coming to the main project from a different angle and with completely new ideas.

I’ve been trying for quite a long to work online with other people on some projects from my home office (which is in the middle of nowhere). As you can guess, it works to a certain point and majority of them were improved upon meeting face to face. And this left me wondering how far can I push online collaborations. It isn’t usually an issue in IT field, but so far it doesn’t look very promising in research.

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Posted by on August 27, 2008 in Comments, Community, Research


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One year of blogging – plans for ten years

Ethos Roundtable at Bob Doyle's Home - July 18...Image by Pathfinder Linden via Flickr

Following BioBarCamp I missed one year anniversary of this blog. With sixty something posts I cannot say I’m very productive blogger, but I didn’t aim at being one, as probably all other science-types. My goal was to be engaged in the conversation and I have reached it much faster than I expected. I got lots of help and encouragement from people I wouldn’t even dear to email a year ago. I know much more than I did on things outside of my research area. While it sounds all pathetic, advantages of being part of this community are hard to overestimate – I wrote about it couple of times already (and Neils did a great job summarizing why you should have a web presence).

Where is “Freelancing science” heading? That’s a question I asked myself pretty often during last 12 months. At first, I just blogged about interesting stuff around bioinformatics. Then I made a jump into freelancing as scientists (and this experiment goes pretty well). Statistics on keywords people are using to find this blog clearly show that there’s some interest within bioinformatics community in following this path. But the idea for this blog I have right now is not about freelancing anymore. Or rather it’s about freelancing on the next level, because today I think about starting a non-profit institute.

I believe that small research groups formed as a non-profit organizations will have enourmous impact on science within next ten, twenty years (more about it in upcoming post about the future of scientists). In spirit of freelancing they will jump from one project to another (see Deepak’s post about bursty work and follow-ups), developing solutions and making discoveries much faster (or cheaper) than it is possible in beaurocratic environment. We do have tools for effective collaboration online, we have new generation scientists that do not feel attached to academic system and we have science which starts to evolve about undestanding data, not performing experiments. Is it time to try such approach?

So, watch this space to see how the idea develops. I’m also interested in your opinions and experiences with starting and cooperating with non-profits if you have any.

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Posted by on August 11, 2008 in Career, Community, Research


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