Author Archives: Marco Barnig

OpenWorm Caenorhabditis elegans

Posted on by

Last update : September 4, 2024

OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (often called C. elegans, even if this term is a species abbreviation), a free-living, transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance.

OpenWorm background

Research into the molecular and developmental biology of C. elegans was begun in 1974 by Nobel prize laureate Sydney Brenner and it has since been used extensively as a model organism for development biology. Sydney Brenner founded the Molecular Sciences Institute in Berkeley, California.

Caenorhabditis elegans (Wikipedia)

Caenorhabditis elegans (Wikipedia)

The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, and collagenous cuticle. C. elegans has two sexes: hermaphrodites and males (0.05%).

C. elegans is one of the simplest organisms with a nervous system. In the hermaphrodite, this comprises 302 neurons whose pattern of connectivity (connectome) has been completely mapped and shown to be a small-world network. C. elegans was also the first multicellular organism to have its genome completely sequenced. The genome consists of six chromosomes (named I, II, III, IV, V and X) and a mitochondrial genome. The sequence was first published in 1998 with regular updates, because DNA sequencing is not an error-free process. The latest version released in the WormBase () is WS238.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, Lincoln Stein of the Ontario Institute for Cancer Research, and John Spieth of the Washington University Genome Sequencing Center. Richard Durbin served as a principal investigator until 2010.

Additional informations about C. elegans are available at the following links :

  • WormBook – a free online compendium of all aspects of C. elegans biology
  • WormAtlas – an online database for behavioral and structural anatomy of C. elegans
  • WormClassroom – an education portal for C. elegans
  • WormImage – thousands of unpublished electron micrographs and associated data
  • WormWeb.org – an interactive cell lineage and neural network
  • Cell Exlorer – a 3D visualization tool for the structural anatomy of C. elegans
  • C. elegans movies

OpenWorm open source project

Despite being extremely well studied in biology, the C. elegans still eludes a deep, principled understanding of its biology. The OpenWorm project uses a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, the data available in the scientific community is incorporated into OpenWorm software models.

An open-source simulation platform called Geppetto is used by the OpenWorm Project to run these different models together. An OpenWorm Browser enables ready access to a cell-by-cell 3D representation of the nematode C. elegans in a WebGL enabled browser. The 3d browser was created with the help of the Google Labs Body Browser team. The browser has also been ported to an iOS app to support the project. All the code produced in the OpenWorm project is Open Source and available on GitHub.

The OpenWorm project was realized by a highly motivated group of individuals who believe in Open Science.

The early core team members of the OpenWorm project were :

Bibliography

Neuromorphic computing

Posted on by
neuromorphic computing by Spike Gerrell

credit : Spike Gerrell for the Economist

Neuromorphic computing is a concept developed by Carver Mead, describing the use of very-large-scale integration (VLSI) systems containing electronic analog circuits to mimic neuro-biological architectures present in the nervous system. Carver Mead is a key pioneer of modern microelectronics.

Today the term neuromorphic is used to describe analog, digital, and mixed-mode analog/digital VLSI and software systems that implement models of neural systems. Neuromorphic computing is a new interdisciplinary discipline that takes inspiration from biology, physics, mathematics, computer science and engineering to design artificial neural systems and autonomous robots, whose physical architecture and design principles are based on those of biological nervous systems.

The goal is to make computers more like brains and to design computers that have  features that brains have and computers do not have up to now :

  • low power consumption (human brains use about 20 watts)
  • fault tolerance (brains lose neurons all time without impact)
  • lack of need to be programmed (brains learn and change)

An important property of a real brain is that each neuron has tens of thousands of synaptic connections with other neurons, which form a sort of small-world network. Many neuromorphic chips use what is called a cross-bar architecture, a dense grid of wires, each of which is connected to a neuron at the periphery of the grid, to create this small-world network. Other chips employs what is called synaptic time multiplexing.

The Economist published a few days ago a great article “Neuromorphic computing – The machine of a new soul” with illustrations from the London-based illustrator Spike Gerrell.

Some neuromorphic computing reletad projects are listed below :

Neuromorphic computing is dominated by European researchers rather than American ones. The following links provide additional informations about neuromorphic computing related institutions and topics :

Artificial General Intelligence

Posted on by

Last update : August 7, 2013

Artificial General Intelligence (AGI) is an emerging research field aiming at the building of thinking machines; that is, general-purpose systems with intelligence comparable to that of the human mind (and perhaps ultimately well beyond human general intelligence). While this was the original goal of Artificial Intelligence (AI), the mainstream of AI research has turned toward domain-dependent and problem-specific solutions; therefore it has become necessary to use a new name to indicate research that still pursues the Grand AI Dream. Similar labels for this kind of research include Strong AI, Human-level AI, etc. Other AI researchers prefer the term of Synthetic Intelligence.

The research on AGI is interdisciplinary, focused on whole systems and includes scientific and philosophical investigation and software engineering.

Artificial General Intelligence Research Institute

The term AGI was first used by Mark Avrum Gubrud in November 1997. Fifty years after the launch of the Artificial Intelligence Project in Dartmouth in 1956, Ben Goertzel, Phil Goetz, Pei Wang and Bruce Klein organized the first Artificial General Intelligence Research Institute (AGIRI) workshop in May 2006 to bridge the gap between narrow AI and general-purpose AI. The AGI Research Institute was founded in 2001 with the mission to foster the creation of powerful and ethically positive Artificial General Intelligence. The institute is sponsored by Novamente LLC.

The aspects of Artificial General Intelligence are explained by Pei Wang and Ben Goertzel  in the introduction of their book Advances in Artificial General Intelligence (IOS Press, 2007).

The first conference on Artificial General Intelligence (AGI-08) was organized by AGIRI in March 2008 in Memphis, Tennessee, USA, in association with the Association for the Advancement of Artificial Intelligence (AAAI).

Artificial General Intelligence Society

Ben Goertzel, Pei Wang, Joscha Bach and others founded in September 2011 the Artificial General Intelligence Society (AGI society), a nonprofit organization with the following goals:

  • promote the study of artificial general intelligence (AGI), and the design of AGI systems
  • facilitate co-operation and communication among those interested in the study and pursuit of AGI
  • hold conferences and meetings for the communication of knowledge concerning AGI
  • produce publications regarding AGI research and development
  • publicize and disseminate by other means knowledge and views concerning AGI

The organization of the annual Artificial General Intelligence conference series, which was started in 2008 by AGIRI, has been taken over by the AGI society. The next conference (AGI-2013) will be held in Beijing, China, July 31 – August 3, 2013.

Some additional informations about AGI are available at the following links :

More links are provided in the updated post about Artificial Intelligence.

A look inside mice brains

Posted on by

A team of researchers at the Stanford University, lead by Mark Schnitzer, an associate professor of biology and applied physics, planted tiny probes inside mice brains to detect what were essentially mouse memories. The study was published February 10, 2013, in the online edition of Nature Neuroscience.

inside mice brains

Read a mouse’s mind

The experiment involved the insertion of a needlelike microscope into the hippocampus of the mice brains. The microscope detected cellular activity and broadcast digital images through a cell phone camera sensor that fit like a hat over the heads of the critters as they were running around. Over the course of a month, the scientists were able to document patterns of activity in about 1000 neurons of the mice brains where they store long-term information. To get the results, an engineered gene was injected into the mice brains so that their proteins were sensitive to calcium ions. That caused the magnified cells to light up on the computer screen in flashes of green fluorescence when the neurons were activated.

Three students, who worked on the project, have formed a startup company called Inscopix, and they plan to sell the technology to neuroscience researchers.

[jwplayer player=”1″ mediaid=”13056″]

More informations are available at the news website of Stanford University.

Synthetic Biology

Posted on by

Synthetic biology is the design and construction of new biological parts, devices, and systems, and the re-design of existing, natural biological systems for useful purposes. It combines biology and engineering with a focus on Biotechnology.

Synthetic biologists focus on finding how life works (the origin of life) or how to use it to benefit society, including the approach of biology by inserting man-made DNA into a living cell and the approach of chemistry by working on gene synthesis as an extension of synthetic chemistry.

The website syntheticbiology.org, originally started by a group of students, faculty and staff from MIT and Harvard, now regroups all individuals, groups and labs from various institutions who are committed to engineering biology in an open and ethical manner. The site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.

An exciting synthetic biology project was recently funded succesfully on Kickstarter : Glowing Plants: Natural Lighting with no Electricity. A few days ago, without explanation, Kickstarter quietly altered its guidelines for project creators, introducing a new term that bans creators from giving away genetically-modified organisms (GMOs) as rewards to their online backers (see the post Kickstarter bans project creators from giving away genetically-modified organisms edited by Duncan Geere at The Verge website).

More informations about synthetic biology are available at the following links :

Kickstarter projects

Posted on by

Last update : October 6, 2018

Kickstarter is a new way to fund creative projects. It’s a crowdfunding platform for everything from films, games, and music to art, design, and technology. Since the launch in 2009, more than 12 million people have pledged over 2.8 Billion dollars, funding more than 118.000 creative projects. Project creators set a funding goal and a deadline. If people like a project, they can pledge money to make it happen. Funding on Kickstarter is all-or-nothing : projects must reach their funding goals to receive any money. To date, 36% of projects have reached their funding goals. Backers are supporting projects to help them come to life, not to profit financially. Instead, project creators offer rewards to thank backers for their support.

A Kickstarter app for mobiles is available at the AppStore.

I am a backer for the following projects :

Kickstarter Account Page

Kickstarter Account Page with backed projects

Here is a list of further projects which I consider very interesting :

Links

Supertoy Teddy and Huggable

Posted on by
Supertoy Teddy

Supertoy Teddy

Supertoy Teddy is the world’s first talking teddy with a mind of its own and the ability to hold real conversations with those who speak to it. It has been developed by Ashley Conlan (CEO of Supertoy Robotics) and Kartsen Fluegge (CEO of Pannous GmbH), the creators of the successful app Jeannie, the Siri style chatbot that has been downloaded over 3 million times on mobile devices.

Supertoy Teddy uses artificial intelligence (AI). A smartphone acts as its brawn and the internet server as its brain. Supertoy Teddy’s robotic mouth moves in synchronization to what it says and inbuilt speakers enhance the volume of its voice. Role play will be added to the Supertoy Teddy and several costumes and dresses will be sold at the online shop.

The robot’s hardware is simple: just an audio in/out interface and a motor for mouth animation. Supertoy Teddy connects via standard audio plug to an iOS or Android device. Asley Conlan suggests putting the phone inside the Supertoy for realism. The magic is in the software, which has evolved from the popular Jeannie chatbot app.

[jwplayer player=”1″ mediaid=”12984″]

The creators of Supertoy Teddy have started a Kickstarter campaign for crowdfunding during the funding period July 24, 2013 – August 23, 2013. I am one of the bakers of the project.

Huggable (MIT)

Huggable (MIT)

Huggable is a similar type of robotic companion that has being developed at the MIT Media Lab (Personal Robots Group) for healthcare, education, and social communication applications a few years ago. The early technical development of the Huggable was supported in part by a Microsoft iCampus grant in 2006.

Crowdfunding and crowdsourcing

Posted on by

Last update : September 24, 2013

Crowdfunding is the application of the Crowdsourcing concept to the collection of funds through small contributions from many parties in order to finance a particular project or venture. Crowdsourcing is the practice of obtaining needed services, ideas, or content by soliciting contributions from a large group of people, and especially from an online community, rather than from traditional employees or suppliers.

The First AAAI Conference on Human Computation and Crowdsourcing will be held November 7-9, 2013 in Palm Springs, California, USA.

Crowdfunding is alternately called crowd financing, equity crowdfunding or crowd-sourced fundraising.

An early precursor of the crowdfunding business model was Praenumeration, a common business practice in the 18th century book trade in Germany.

Crowdfunding is not only used to fund a startup company (equity-based crowdfunding), but also to create artworks such as music, theater, dance, films, literature and technology.

Crowdfunding platforms bring together the project initiator and the crowd. They create the necessary organizational systems and conditions for resource integration among all the players to take place. There are over 450 crowdfunding platforms with fundamental differences in the services provided. A comparison of crowd funding services is available at Wikipedia.

Some examples of crowdfunding platforms are listed below :

Since soliciting investments from the general public is often illegal in most countries, unless the opportunity has been filed with an appropriate securities regulatory authority, traditional crowdfunding platforms treat funds as donations. In the U.S. the crowdfunding exemption movement has been successful in 2012 with the passage of the Jumpstart Our Business Startups Act or JOBS Act,  a law intended to encourage funding of small businesses by easing various securities regulations.

In the past capital for startup companies has mainly been provided by business angels (also known as angel investors), in exchange for convertible debt or ownership equity. An increasing number of angel investors organize themselves into angel groups or angel networks to share research and pool their investment capital, as well as to provide advice to their portfolio companies.

Some angel networks in Luxembourg and the Greater Region are listed hereafter :

  • Luxembourg Business Angel Network (LBAN)
  • Seed4Start
  • EBAN (pan-European representative for the early stage investor community)

Here are some links to selected crowdfunding projects :

RoboRoach : control a living insect

Posted on by
RoboReach image

RoboR0ach image

RoboRoach is is the world’s first commercially available cyborg. Cockroaches use the antennas on their head to navigate the world around them. When these antennas touch a wall, the cockroach turns away from the wall. The antenna of a cockroach contains neurons that are sensitive to touch and smell. These neurons convey information back to the brain using electricity in the form of spikes. To control cockroaches, microstimulation (neurotechnology) can be used by sending small electrical pulses directly to the neurons of the cockroach antennas via a backpack. A learning kit, called RoboReach kit, has been created by neuroscientists, engineers and educators of the University of Michigan. The cockroach undergoes a short surgery in which wires are placed inside the antenna. Once the insect recovers, a backpack is temporarily placed on its back.

RoboRoach

RoboRoach photo

Tim Marzullo and Greg Gage of the University of Michigan founded Backyard Brains, a small company that makes neuroscience educational equipment and experiments for students of all ages. Backyard Brains terminated succesfully in July 2013 a Kickstarter campaign to support the RoboRoach Kit.

Of course, there are underlying ethical questions attached to such experimentation involving living things. People don’t always recognize insects as valuable life forms, but some critics are already speaking out against RoboRoach. Animal rights group PETA has spoken of the project as retrogressive and morally dubious.

In defence of the cockroach: RoboRoach Kickstarter ignores ethics is the title of a contribution posted by Liat Clark in wired.co.uk.

Backyard Brain has responded to criticisms with this statement on its website:
Our experiments are not philosophically perfect and without controversy; however, we believe the benefits outweigh the cost due to the inaccessibility of neuroscience in our current age.

[jwplayer player=”2″ playlistid=”13026″ aspectratio=”62:53″]

Backyard Brains sells other products in their online shop : Spikerbox, EMG Spikerbox, Completo, 3D manipulator, RoachScope.

W3C : World Wide Web Consortium

Posted on by

Last update : June 30, 2014

The W3C (World Wide Web Consortium) is an international community where Member organizations, a full-time staff, and the public work together to develop Web standards. Led by Web inventor Tim Berners-Lee and CEO Jeffrey Jaffe, W3C’s mission is to lead the Web to its full potential.

The W3C Team includes 85 people working from locations across the globe. W3C is hosted by the Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory (MIT/CSAIL) in the United States, at the European Research Consortium for Informatics and Mathematics (ERCIM) in Sophia-Antipolis in France, at the Keio University Shonan Fujisawa Campus (SFC) in Japan and at the Beihang University in China.

Most W3C work revolves around the standardization of Web technologies. To accomplish this work, W3C follows processes that promote the development of high-quality standards based on the consensus of the community. The W3C is founding member of OpenStand (The Modern Paradigm for Standards), an open, collective movement to radically improve the way people around the globe develop, deploy and embrace technologies for the benefit of humanity.

W3C standards define an Open Web Platform for application development that has the unprecedented potential to enable developers to build rich interactive experiences, powered by vast data stores, that are available on any device. HTML5 will be the cornerstone for this platform, combined with other technologies including CSS, SVG, WOFF, the Semantic Web stack, XML, Javascript and a variety of APIs.

The W3C standards are grouped as follows :

eGovernment (Better Government Through Better Use of the Web) is also a topic at W3C.

A comprehensive documentation for developers about the Open Web Platform is available at the community-run source Web Platform Docs (currently in alpha version).

W3C standards are written by temporary working groups formed by W3C members and invited experts. Membership in W3C is open to all types of organizations (including commercial, educational and governmental entities) and individuals. For Luxembourg, annual membership fees vary between 1.950 and 68.000 EUR.

Currently there are about 50 working groups listed at the W3C website. There are also special interest groups (forum for the exchange of ideas) and coordination groups (to manage dependencies and facilitates communication with other groups).

W3C has chartered two permanent groups :

  • The Technical Architecture Group (TAG) documents and builds consensus around principles of Web architecture.
  • The Advisory Board (AB) provides ongoing guidance to the Team on issues of strategy, management, legal matters, process, and conflict resolution.

To meet the needs of a growing community of Web stakeholders, W3C has created Community and Business Groups. Community Groups enable anyone to socialize their ideas for the Web at the W3C for possible future standardization. Business Groups provide companies anywhere in the world with access to the expertise and community needed to develop open Web technology. New W3C Working Groups can then build mature Web standards on top of best of the experimental work, and businesses and other organizations can make the most out of W3C’s Open Web Platform in their domain of interest.

Community Groups are designed to promote innovation and to lower barriers to individual participation. Anyone may participate without fees in community groups. Currently there are about 130 community groups. I am mainly interested in the following community groups :


In the past some web communities were created outside of the W3C, with similar goals. One example is the Web Hypertext Application Technology Working Group (WHATWG) which was founded in 2004 by individuals from Apple, the Mozilla Foundation and Opera Software in response to the slow development of W3C web standards and W3C’s decision to abandon HTML in favor of XML-based technologies. On March 7th, 2007, the W3C publicly announced that they are restarting an HTML specification effort. A W3C HTML working group was created and stated : “The HTML Working Group will actively pursue convergence with WHATWG, encouraging open participation within the bounds of the W3C patent policy and available resources”. (see WHATWG Blog)