From 2014.igem.org

Revision as of 05:58, 17 October 2014

Abstract

iGEM@home is a distributed computing platform build upon the BOINC framework. Volunteers download a client software that receives and runs work packages distributed from a central server. Combining the computational capacity of at least hundreds of personal computers, this approach allows (1) future iGEM teams to run heavy computations without the need of access to a big server cluster and (2) offers the opportunity to spread information about Synthetic Biology and iGEM events and projects. By actively promoting the platform and constantly motivating a growing community of iGEM@home supporters, we managed to accumulated ca 1 TeraFLOPS of computational power and displayed about 40,000 screensaver slides to more than 400 community members. We conducted a survey for evaluation and found our project content well received by the community: 80% of first time BOINC users was also interested in the information on synthetic biology and over 60% of the users had never heard of iGEM before and got involved into synthetic biology via iGEM@home. The succes of the project was reflected and stimulated by the national and international press.

If you want to know more about the software that we developed please visit our Software Overview page, if you are rather interested in the modelling that we ran on iGEM@home and how it relates to our project, please visit the Linker modeling page.

Introduction

The creative concepts developed and the plethora of information gathered during the last decade by iGEM teams from all over the world proof efforts in Human Practices worth to be rewarded with a track of its own $Link in this year’s iGEM competition. Since iGEM teams from Heidelberg have always been interested in the question how laymen citizens can get involved into synthetic biology, they already introduced new concepts to the community to improve communication (first abstract page in multiple languages, first site tour for laymen, first mascot 2008), to do research on the mechanisms of science communication (2010) and to encourage reflection by philosophers and artists as representers of society (2010, 2013). Following the findings of our former team mates , also supported by literature as described [http://www.sciencedirect.com/science/article/pii/S0016328713000384 here], that acceptance towards a technology is not correlated with the information provided to a sceptic public, we rather aim at involving the public into the creative process of scientific work. In the style of the new iGEM community labs track that encourages science amateurs to contribute “beyond the accolades of scientific publishing and economic reward”, we sought for a new way to involve laymen in actual science and build a strong community of well informed supporters and communicators of synthetic biology at the same time. Thereby we want to lay the foundation for a democratization of Science in an enlightened society. Now we proudly present the crowdsourcing and communication platform iGEM@home!

Introducing Distributed Computing to the iGEM community

Modern biology uses computational simulations of models for validation as well as to predict key experiments and suitable designs for specific applications. Despite of the fact that the experience with and the mere amount of algorithms and code dedicated to biological systems is growing exponentially these days, big data evaluation such as sequence analysis and multidimensional problems such as protein folding still consume vast amounts of computational resources. Therefore main aspects of biological science are only accessible to research institutions that provide these resources in form of supercomputers or computer clusters. In order to open computational biology up to all future iGEM teams in a manner that is not dependant of institutional affiliations, we decided to develop a platform from a set of applications that build upon the BOINC framework for distributed computing $Link. Thereby we provide access to computing power for future (community lab) iGEM teams and at the same time create an opening for laymen to jump in and empower science! $Link

BOINC and iGEM - Foundations of a rewarding relationship

The BOINC framework distributes computational tasks to volunteers who provide computational resources in form of calculation time spent by the CPU of their idling personal computers. Volunteers download and install a client software that receives work packages from a central server unit and runs calculations once the computer is not in use. Alternatively users may dedicate a certain percentage of their computing power to destributed computing projects that they like to support. After the successful execution of the computation the result is uploaded to our server. One of the best known distributed computing projects is [http://setiathome.ssl.berkeley.edu/ SETI@home], a project in which volunteers contribute computing power to the search for extra-terrestrial intellegance. In our case the need for computing power arose from the calculations needed to evaluate the linker model that provides rigid linkers for the circularization of proteins $LInk. In both cases the contributors are rewarded with points that reflect the computing time already spent and the dedication towards certain projects. In order to take motivation to the next level we implemented a platform that allows to feed information to the BOINC screensaver (figure 1). Thereby we enable iGEM teams from all over the world to reach an interested and motivated audience with information about their projects, Human Practices activities and iGEM and Synthetic Biology in general. In return users of iGEM@home will be rewarded with informations and insights into one of the most vital communities in science that catch their attention in the very moment they get back to their computers.

Outreach

The need to build a vivid community is key to run a successful distributed computing project. As the project depends on the voluntary support of people it is important to get people enthused about the science behind the project, so they are willing to support the project. Good communication is therefore essential to find support. We therefore used different channels to present and promote our project and iGEM in general to convince people to help us - which in the end turned out to be key to one of our biological main projects!

The Communication Platform iGEM@HOME

The important job after convincing the user to try our software, is to convince them to continuously support us by constantly feeding them with interesting facts on iGEM and offering them ways to influence the project.

Forum: Feedback on Computing and Projects

The first pillar for the communication is an integrated [http://www.igemathome.org/igemathome/forum_index.php forum] software, that serves several purposes: First of all, additional information like status updates or information on the biological projects can be communicated to the community via the 'News' and 'Science' sections of the forum. In addition the users can give elaborate feedback on problems arising from the client site. Finally user forums are an integral component to the BOINC distributed computing community and are widely used to present user achievments such as the number of projects supported, computational time spent to projects, BOINC points rewarded for computing and also to compare the stats of different projects [http://boincstats.com/en/stats/projectStatsInfo projects]. Forum users are provided with a personal profile that displays memberships in BOINC teams, points earned for computing and the possibility to contact other users via private text messages.

Screen Saver: Communication Channel for Synthetic Biology

The second pillar of our communicational concept is a browser page that feeds content to the [http://www.igemathome.org/screensaver screensaver] implemented into BOINC. We decided to post different types of content: (1) General information about (synthetic) biology, (2) general facts about the iGEM competition, (3) presentations of iGEM team projects, (4) announcements of special events that are open to public organised by iGEM (Human Practices) teams. We started with a small series of 'Did you know ...?' pages, presented the project of iGEM team Heidelberg 2013 and contacted other iGEM teams to offer the opportunity to present content to a growing community of iGEM supporters. In order to test the capabilities of iGEM@home as a communication channel, we announced our own events via the channel. A final test will be carried out after wiki freeze by announcing an event exclusively via the screensaver (see a short description in the 'Outlook' section at the end of this text). Last not least we can announce that we received content from two cooperating iGEM teams that we proudly present in our screensaver: Team Marburg sent a flyer for their 'iGEM Quiz Marburg' and the Berlin team sent in a text and figures on their project on 'Magnetic E.coli'.

Some example pages of the iGEM@home screensaver: