Category: science

Quantifying cost-effectiveness of scientific cloud computing in genomics and beyond

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Biosystems Analytics

On-demand computing, often known as “cloud computing” provides access to the computing power of a large data center without having to maintain an in-house high performance computing (HPC) cluster, with attendent management and maintenance costs.  As even the most casual observers of the tech world will know, cloud computing is growing in any many sectors of the economy, including scientific research.  Cheap “computing as a utility” has the potential to bring many large-scale analyses within reach of smaller organizations that may lack the means or infrastructure to run a traditional HPC.  These organizations or individuals could include smaller clinics, hospitals, colleges, non-profit organizations and even individual independent researchers or groups of researchers.  But beyond the industry enthusiasm, how much can cloud computing really help enable low-cost scientific analyses?

There is now a veritable smorgasbord of offerings from many different vendors, but the big players are Amazon…

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Academic publishing for fun and profit

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Anthropologist David Graeber recently tweeted: “doing online research is SO much harder than it was when I was writing Debt. Everything’s being privatised. It’s a disaster for scholarship.”  The book he’s referring to is  Debt: The First 5000 Years, his groundbreaking book on the history of debt, from ancient times to the present debt crisis, first published back in ye olde 2011.  If things are bad in the humanities, over in the sciences, things aren’t much better:  The Digital Biologist, has published a particularly detailed and trenchant post on the current state of scientific academic publishing.  Worth a read:

The eye-watering prices that these academic publishing companies charge for their journals play a considerable role in further draining public money from a research system that is already enduring a major funding crisis. By some estimates, the subscriptions that universities must pay for access to these journals swallow up  as much as 10% of the public research funding that they receive.  This public money is essentially being channeled away from research and into the coffers of private sector corporations.

….

It is a testament to how expensive access to these journals has become, that even Harvard University, one of the wealthiest institutions of higher education in the world, recently sent a memo to its faculty members informing them that it could no longer afford the price hikes imposed by many large journal publishers.

Read more at: The Digital Biologist…

Framing climate change as a national security issue has it’s perils

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It’s good to see that climate change as a serious issue has returned to US electoral politics (albeit completely on one side of the aisle at this point). However it’s return is being framed in a particular way: using the language of national security.  After past efforts to use environmental, public health and economic security arguments have failed to gain the necessary amount of traction to change policy, supporters of action on climate change believe they may be now on to a winner.  In the recent Democratic primary debate, Senator Bernie Sanders suggested that climate was not just a “national security” issue, but the biggest national security issue.  While framing climate change this way has clear advantages: it gives the issue a sense of urgency and purpose, and it can perhaps convince more hawkish types to take the issue seriously, it is not without certain perils.

In an interesting piece by in Wired, dissecting this new approach, one professor of public policy notes that using national security metaphors:

…reinforces nationalistic responses to solving the problem, as opposed to collective efforts that might be mutually beneficial to the world

In a sense climate change is the ultimate collective action problem, and piecemeal national security responses are likely to run more towards local (or national) mitigation of the effects of climate change, rather long-term systemic changes in the global economy that will be needed to effectively tackle the problem.  So if the “national security” rhetoric takes off, environmentalists, politicians and scientists will want to be sure that the other dimensions of climate change policy aren’t abandoned or ignored.

Read more at Wired

(h/t to Tim De Chant of Per Square Mile)

Biologist Mickey von Dassow on collaboration, citizen science and ctenophores

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Biosystems Analytics

Mickey von Dassow is a biologist who is interested in exploring how physics contributes to environmental effects on development. He created the website Independent Generation of Research (IGoR) to provide a platform to allow professional scientists, other scientists, non-scientists or anyone to collaborate and pursue any scientific project that they are curious about. I talked to him recently about his new site, citizen science and the future of scientific research and scholarship.

Mickey_headshot Mickey von Dassow

Can you describe your background?

My background is in biomechanics and developmental biology. My Ph.D. asked how feedback between form and function shapes marine invertebrate colonies. During my postdoc I worked on the physics of morphogenesis in vertebrate embryos, specifically focusing on trying to understand how the embryo tolerates inherent and environmentally driven mechanical variability. Since then I have been independently investigating interactions among ecology, biomechanics, and development of marine invertebrate embryos, as…

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Gut check: autocatalytic sets meets systems biology

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Biosystems Analytics

A truly systems view of life must account for the remarkable property that cells maintain and reconstitute themselves in the face of a constant turnover of chemical and molecular components.  Much research done under the rubric of systems biology rarely tackles this thorny dynamical problem directly, tending to largely focus on modeling of individual elements or pathways, or examining genome-wide, generally static, patterns.  Partly this is due to the sheer complexity of even the simplest cell, partly because the data is still sparse, and partly because many of the theoretical constructs are not easily accessible or intuitive to most biologists.

wpid-wp-1443203318157.jpeg“Autocatalytic sets” are one of several systems-level models developed to explain both the self-maintenance phenomenon and have also been used as possible models for the origin of life, having been introduced several decades ago by Stuart Kauffman.   These concepts and models but have been extended considerably…

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What innovation isn’t

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Biosystems Analytics

Innovation.  It’s as American as apple pie.  From the US President on down, everybody is talking about innovation.  From university presidents and corporate leaders to Silicon Valley tycoons, all agree that we need more of it.  Airport bookstores have walls of books on innovation: a quick search on Amazon resulted in 70,140 titles containing the word “innovation”, 711 of which were published in the last 90 days alone.  Many of them are little more than generic business advice books with the word “innovation” shoehorned into the title, including gems such as Creating Innovation Leaders (earning bonus points for including buzzwords “leadership” and “creativity”).  So it was with some trepidation that I recently picked up Scott Berkun’s The Myths of Innovation – first published in 2007 – and found it had a refreshing and unpretentious take on the subject.  Since it has become such an overused buzzword, Berkun argues that…

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All Big Data is equal, but some Big Data may be more equal than others

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Biosystems Analytics

We are in the era of Big Data in human genomics: a vast treasure-trove of information on human genetic variation either is or will soon be available.   This includes older projects such as the HapMap, and 1000 Genomes to the in-progress 100,000 Genomes UK.  Two technologies have made this possible: the advent of massively parallel “next generation” sequencing where each individuals’ DNA is fragmented and amplified into billions of pieces; and powerful computational algorithms that use these fragments (or “reads”) to identify all the “variants” – any changes that are different to the “reference genome” – in each individual.

With existing tools this has become a relatively straightforward task.  Identification of single nucleotide polymorphisms or variants (SNVs) – single base differences between the individual and the reference genome – especially medically relevant ones –  is beginning to become routine. A project I worked on with…

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Finding data in the long-tail

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Biosystems Analytics

blog_1_fig_1Scientists are increasingly examining the most comprehensive catalogue of datasets for any particular question.  Making sure you can find as much of the data relevant to a particular problem thus begins to loom as a large issue.   Although institutional repositories (such as NCBI, Dryad, Figshare etc.) are great at storing the final published versions of the data sets, some early and smaller-scale research data can get lost in the “long-tail“.   Anne Thessen has a great post over on her blog on the Data Detektiv, on how to locate and keep track of such “dark data”:

Finding relevant data, especially if the needed data are dark, can be a difficult and lengthy task. … Was there a way to discover data based on events earlier in the research workflow? After some thought, I realized that databases and lists of awards made by funding agencies were an…

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Volvocine algae relationship status: “It’s complicated”

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Biosystems Analytics

800px-Mikrofoto.de-volvox-4Volvox are green algae that can form large and amazingly beautiful colonies of up to 50,000 cells, and have been widely studied as a model for the evolution of multicellularity, but they also have a huge diversity of mating systems.   Matthew Herron has a great post over on his blog, Fierce Roller (which focuses on the the biology of volvocine algae and evolutionary mathematical models amongst other things), about the unusual and complicated world of Volvox sex, direct from the the Volvox 2015 conference.   For those of us who work mostly on model organisms, it’s good to be reminded that these organisms are just the tip of the proverbial evolutionary iceberg, and that there are many great practical and conceptual discoveries awaiting all over the tree of life.

Volvox, and the volvocine algae in general, are well known as a model system for the evolution of multicellularity and cellular…

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