OpenWorm Caenorhabditis elegans

Last update : August 9, 2013

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
  • WormImagethousands of unpublished electron micrographs and associated data
  • – 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 is realized by a highly motivated group of individuals who believe in Open Science. The OpenWorm website includes a Blog, a Wiki, a FAQ and Donate page, lists about milestones, projects, events, publications, getting started and getting involved resources and more.

The core team members of the OpenWorm project are :

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Artificial General Intelligence

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.

PAL : personalized assistant that learns

cognitive assistant

DARPA PAL program

The DARPA PAL (the Personalized Assistant that Learns) program focused on improving the way that computers support humans through the use of cognitive systems. These are systems that reason, learn from experience and accept guidance in order to provide effective, personalized assistance. DARPA’s five-year contract (2003 – 2008) brought together over 300 researchers from 25 of the top university and commercial research institutions, with the goal of building a new generation of a cognitive personalized assistant that can reason, learn from experience, be told what to do, explain what they are doing, reflect on their experience, and respond robustly to surprise. Among the contributors were the Carnegie Mellon University, the University of Massachusetts, the University of Rochester, the Institute for Human and Machine Cognition, Oregon State University, the University of Southern California, and Stanford University, as well as from SRI.

SRI International has led the PAL Framework effort to make available many of the successful machine learning and reasoning technologies developed on the PAL program for use by the broader DARPA, research, and military communities. SRI was founded as Stanford Research Institute in 1946 and is a nonprofit research institute headquartered in Menlo Park, California. The institute formally separated from Stanford University in 1970 and is now one of the largest contract research institutes in the world.

One of the components of PAL was CALO (Cognitive Assistant that Learns and Organizes), an artificial intelligence project that attempted to integrate numerous AI technologies into a cognitive personalized assistant. The CALO effort has had many major spin-offs :

  • the Siri intelligent software assistant that is now part of the Apple iOS
  • the news aggregation service Trapit
  • the artificial intelligence-enhanced calendar application for iOS, Tempo AI
  • the travel guide app Desti

Artificial Intelligence

Last update : August 9, 2013

Artificial intelligence (AI) is the intelligence of machines and the branch of computer science which aims to create it.The term was coined by John McCarthy in 1955. The field of AI research was founded at a conference on the campus of Dartmouth College in the summer of 1956. The attendees, including John McCarthy, Marvin Minsky, Allen Newell and Herbert A. Simon, became the leaders of Artificial Intelligence research for many decades.

Good Old-Fashioned Artificial Intelligence (GOFAI)

AI research began in the mid 1950s after the Dartmouth conference. The field AI was founded on the claim that a central property of humans, intelligence, can be so precisely described that it can be simulated by a machine. The first generation of AI researchers were convinced that this sort of AI was possible and that it would exist in just a few decades.

In the early 1970s, it became obvious that researchers had grossly underestimated the difficulty of the project. By the 1990s, AI researchers had gained a reputation for making promises they could not keep. The AI research suffered from longstanding differences of opinion how it should be done and from the application of widely differeing tools.

The field of AI regressed into a multitude of relatively well insulated domains like logics, neural learning, expert systems, chatbots, robotics, semantic web, case based reasoning etc., each with their own goals and methodologies. These subfields, which often failed to communicate with each other, are often referred as applied AI, narrow AI or weak AI.

The old original approach to achieving artificial intelligence is called GOFAI. The term was coined by John Haugeland in his 1986 book Artificial Intelligence: The Very Idea.

Weak Artificial intelligence

After the AI winter, the mainstream of AI research has turned with success toward domain-dependent and problem-specific solutions. These subfields of weak AI have grown up around particular institutions and individual researchers, some of them are listed hereafter:

Peter Norvig, Google’s head of research, and Eric Horvitz, a distinguished scientist at Microsoft Research, are optimistic about the future of machine intelligence. They spoke recently to an audience at the Computer History Museum in Palo Alto, California, about the promise of AI. Afterward, they talked with Technology Review‘s IT editor, Tom Simonite.

A few AI searchers continue to believe that artificial intelligence could match or exceed human intelligence. The term strong AI, now in wide use, was introduced for this category of AI by the philosopher John Searle of the University of California at Berkeley. Among his notable concepts is the Chinese Room, a thought experiment which is an argument against strong AI.

Strong Artificial Intelligence

Strong AI is the intelligence of a machine that could successfully perform any intellectual task that a human being can. Strong AI is associated with traits such as consciousness, sentience, sapience (wisdom) and self-awareness observed in living beings.

There is a wide agreement among AI researchers that strong artificial intelligence is required to do the following :

  • reason, use strategy, solve puzzles and make judgements under uncertainty
  • represent knowledge, including commonsense knowledge
  • plan
  • learn
  • communicate in natural language
  • integrate all these skills towards common goals

Other important capabilities include the ability to sense (see, …) and the ability to act (move and manipulate objects, …) in the observed world.

Some AI researchers adopted the term of Artificial General Intelligence (AGI) to refer to the advanced interdisciplinary research field of strong AI. Other AI researchers prefer the term of Synthetic Intelligence to make a clear distinction with GOFAI.

The following links provide some informations about the history and the concepts of Artificial Intelligence :

A list of organizations and institutions dealing with Artificial Intelligence is shown below :

“Artificial intelligence is no match for human stupidity!”

Global Brain Metaphor

Last update : August 6, 2013

Global Brain

Global Brain Project

The global brain is a metaphor for the worldwide intelligent network formed by all the individuals of this planet, together with the information and communication technologies that connect them into a self-organizing whole. Although the underlying ideas are much older, the term was coined in 1982 by Peter Russell in his book The Global Brain.

The first peer-refereed article on the subject was written by Gottfried Mayer-Kress and Cathleen Barczys in 1995. The first algorithms that could turn the world-wide web into a collectively intelligent network were proposed by Francis Heylighen and Johan Bollen in 1996. Francis Heylighen reviewed the history of the concept and its usage, he distinguished four perspectives  :

  • organicism
  • encyclopedism
  • emergentism
  • evolutionary cybernetics

These perspectives now appear to come together into a single conception.

Global Brain Group and Institute

In 1996, Francis Heylighen and Ben Goertzel founded the Global Brain Group, a discussion forum grouping most of the researchers that had been working on the subject to further investigate this phenomenon. The group organized the first international conference on the topic in 2001. In January 2012, the Global Brain Institute (GBI) was founded at the Vrije Universiteit Brussel to develop a mathematical theory of the brainlike propagation of information across the Internet. The GBI grew out of the Global Brain Group and the Evolution, Complexity and Cognition research group (ECCO).

The following list provides links to further informations about the global brain :




Bio:Fiction was the world’s first synthetic biology film festival. The first and original festival took place at the Museum of Natural History in Vienna, Austria, from 13-14th of May 2011. Since then Bio:Fiction is officially on tour around the world. The festival provided information and dialogue about synthetic biology in an attractive, factual and entertaining way.

Synthetic biology aims at applying engineering principles to biology. The DNA of an organism is no longer manipulated, but programmed on a computer and built up from scratch.

The Festival marked also the beginning of the synbio art exhibition Synth-ethics in the Museum, that presented biotech art objects related to synthetic biology. The exhibition featured 10 artist and lasted from May 14th to June 26th, 2011.

The exhibition was produced by Biofaction KG and is part of the Cinema and Synthetic Biology project, funded by GEN-AU ELSA.

Strandbeests : Kinetic Sculptures by Theo Jansen

Last update : August 9, 2013


Strandbeest “Animaris Ordis Parvus” Assembly Kit

Theo Jansen, born 14 March 1948, is a Dutch artist and kinetic sculptor. Since 1990 he builds large works, called strandbeests, which resemble skeletons of animals, that are able to walk using wind power on the beaches of the Netherlands. Not pollen or seeds but plastic yellow tubes are used as the basic material of this new creatures. Eventually he wants to put these animals out in herds on the beaches, so they will live their own lives.

Some beach animals  have a stomach consisting of recycled plastic bottles containing air, that can be pumped up to a high pressure by the wind.  Others are able to detect once they have entered water and walk away from it, and one species will even anchor itself to the earth if it senses a storm approaching.

The artworks of Theo Jansen have been presented on numerous websites, TV shows, videos, books, conferences and exhibitions. The movie Strandbeesten, directed by Alexander Schlichter (2008), was presented at the Bio:Fiction festival in 2011.

An assembly kit of a miniature version of the strandbeests Animaris Ordis Parvus is available at the website of the artist. It is produced by Gakken Education Publishing Co. Ltd. Japan.  After assembling, the mini strandbeest walks on the wind, by hand or by blowing against the propeller. Another strandbeest, the mini Rhinocerus, has been published by the same company in Japan.

MMDAgent toolkit

Last update : August 9, 2013



MMDAgent is a toolkit for building voice interaction systems. The toolkit is released for contributing to the popularization of speech technology. Users can design users own dialog scenario, 3D agents, and voices. This software is released under the New and Simplified BSD license. Version 1.3.1 was released on December 25, 2012, and is available at the SourceForge website. The toolkit was created by the Department of Computer Science at the Nagoya Institute of Technology, Japan. The current members of the project team are Keiichi Tokuda, Akinobu Lee and Keiichiro Oura.

MMDAgent  employs MikuMikuDance (MDD) as a foundation for its 3D rendering system, as well as allowing users to maintain a lively conversation with their 3D companion. Hatsune Miku is one of the many models that can be used to hold a conversation with.

MMDAgent speech recognition

The speech recognition module of MMDAgent is based on Julius, the open-source large-vocabulary continuous speech recognition engine. New words to be recognized to MMDAgent can be added by making a user dictionary.

An MMDAgent WordPress Blog with news about the project was launched in August 2012.

AIML (Artificial Intelligence Markup Language)

Last update : July 17, 2013

AIML virtual assistant

Virtual Assistant Denise by Guile 3D Studio

AIML (Artificial Intelligence Markup Language) is an XML-compliant language that’s easy to learn, and makes it possible to customize an artificial intelligence chat robot or creating one from scratch within minutes. AIML is free open-source software provided by the ALICE A.I. Foundation, a non-profit research and training organization. ALICE stands for Artificial Linguistic Internet Computer Entity, an award-winning free natural language artificial intelligence chat robot. The AIML 2.0 draft specification was released on January 16, 2013.

A AIML beginners guide is available at the website of the ALICE  A.I. Foundation.

There are various AIML sets available, among them the free Annotated ALICE AIML set, a revised release of the scripts comprising the award winning chat robot ALICE. The ALICE A. I. Foundation is also offering the commercial version Superbot 2.1 (999 US$) that helps you to create a totally unique custom bot personality for your web site or application.

The other free softwares available are implementations of the ALICE chatbot engine in different computer languages, tools and knowledge bases. Documentation, specifications, tutorials and showcases are available at the website. Chatting with an original ALICEBOT is possible in the Hall of Fame of Digital Art at Leslie’s Artgallery.

Another more advanced implementation of an AIML robot is Denise, a virtual assistant software created by Guile 3D Studio.

An outstanding tool to program a robot brain in AIML is the free GaitoBot AIML editor provided by the german company Springwald Software.


Last update : August 6, 2013

Verbot 5

Verbots (Verbally Enchanted Software Robots)  is a popular chatterbot program and Artificial Intelligence Software Development Kit (SDK) for the Windows platform and for the web, created by Dr. Michael Mauldin and Peter Plantec.

Some milestones of the history of verbots are presented hereafter :

  • 1989 : TinyMUD Gloria
  • 1990 : TinyMUD Julia
  • 1991 : participation of Julia in the first Loebner Prize contest
  • 1994 : chatterbot Julia
  • 1997 : creation of Virtual Personalities, Inc.
  • 2000 : production release of the virtual human interface Sylvie
  • 2004 : release of the Verbot 4 version
  • 2006 : start of Verbots Online
  • 2010 : relase of the Verbot 5 version

Version 4 of verbots was based on MS Agent which has been discontinued by Microsoft in Windows 7.  A properties viewer of MS agents has been created by AbhiSoft Technologies. A related scripting software has been developed by the same company who also provides a file repository for MS Agents.

Version 5 of verbots uses characters made up of 22 SAPI5 viseme groups and animations. The Conversive Character Studio Application allows you to easily create your own talking characters that are compatible with Verbots and VerbotsOnline using high-quality SAPI 5 tts voices. Conversive characters are defined in a .css file in xml format. Sample visemes are available at the verbots wiki website. Animations are a collection of frames which are displayed on the screen in sequence.

The different verbots file types are :

  • ckb : Compiled KnowledgeBase
  • csv : Comma Separated Values
  • vkb : Verbot KnowledgeBase
  • vrp : Verbot Replacement Profile
  • vsn : Verbot Synonyms

The templates to create the Verbots brain are the following :

  • My answers
  • My Knowledge Bases
  • My Design
  • Install

In the Online version you can browse the chat logs, manage your account and list your bot in the online directory. Several tags are available to commande the Verbot. A Verbot editor allows to create and edit the different templates. KnowledgeBases are created from a collection of Rules. Rules contain Inputs and Outputs. Rules can be Primary Rules, Child Rules or Virtual Child Rules. Conditionals, variables and regular expressions are further means to set up a personality. Special inputs allow to start and stop animations, embedded C# code modules allows to execute programs, schedue tags allow to trigger time events, commands are used to open web adresses or to run applications.

The Teaching.vkb KnowledgeBase allows new rules to be dynamically added while chatting.

ChatVerbots for IRC and AIM are available as beta versions.

The following tutorials about Verbots are available :

  • Creating personalities
  • Creating your first rule
  • Creating child rules
  • Knowledge Base templates and csv files

Communities discussing about verbots are listed below :

Concerning  AIML (Artificial Intelligence Markup Language maintained by the Alice Foundation ), verbots don’t comply to this standard. Verbots KB (Knowledge Base) and AIML both are XML based, but the format is different, the working of engine is different, the usability is different.

A free tool to convert AIML files to Verbots KB files is available at the Verbots website.

The Alice Foundation is more active, more dynamic and more professional, compared to the Verbots Community, whereas the Verbots Technology offers some outstanding features.

The Verbots Online Service was closing down at the end of August 2012. Free webhosting for AIML is still available  : Pandorabots for AIML. To fully customize your Bot and to give him a Voice (TTS), a paid subscription is required. SitePal.