Allen Brain Atlas

Paul Allen, the co-founder of Microsoft, funded the development of the Allen Brain Atlas, which lets you navigate visual and genetic information about the brain

The Allen Brain Atlas is a web-based application that is designed to aid the expansion of brain science. Designed and developed in collaboration with an acclaimed group of scientists, the ABA enables users to access an extensive database of ISH images, ABA reference atlas, and gene expression masks. Future releases will allow users to search by gene expression pattern or level, and will contain an expanded gene data set.

source: Allen Brain Atlas, links added.

see also: NCBIWikipedia – Spatiotemporal gene expression

[Photomedia Forum post by T.Neugebauer from Jun 16, 2006   ]

Metamaterials and invisibility

The recent article in Science, Controlling Electromagnetic Fields, by J. B. Pendry from Department of Physics, Blackett Laboratory, Imperial College London, D. Schurig and D. R. Smith from the Department of Electrical and Computer Engineering, Duke University speculate on the use of metamaterials for creating invisibility cloaks

Using the freedom of design that metamaterials provide, we show how electromagnetic fields can be redirected at will and propose a design strategy. The conserved fields–electric displacement field D, magnetic induction field B, and Poynting vector S–are all displaced in a consistent manner. A simple illustration is given of the cloaking of a proscribed volume of space to exclude completely all electromagnetic fields. Our work has relevance to exotic lens design and to the cloaking of objects from electromagnetic fields.

source: science

[Photomedia Forum post by T.Neugebauer from May 26, 2006  ]

Science on television

Closer To Truth (PBS) is a television series that deals with “the fundamental questions of our times explored by creative and thoughtful scientists, scholars and artists.” The video archive contains past debates with scientists on everything from parapsychology, ESP, creativity, consciousness, music and art, etc…

[Photomedia Forum post by T.Neugebauer from Mar 20, 2006   ]

Library of Congress Call Number Sort in PHP

I needed a function that will compare Library of Congress call numbers. I found a function in PERL to do this on Joshua McGee’s site, but I needed it in PHP and our call numbers use a space instead of a period for some of the separators, for example: HA 1107 K49 2003.

Here is the function in PHP:


//is call number $a larger than call number $b?
function locsort ($a,$b)
$pattern =’/^([A-Z]+)\s?(\d+(?:\.\d+)?)\s?([A-Z]*)(\d*)\.?([A-Z]*)(\d*)( (?:\d{4})?)?(.*)?/’;

$i = preg_match($pattern, $a, $regsA);
$j = preg_match($pattern, $b, $regsB);

if (($i==0)||($j==0)) {
return($a > $b);
else {
//if first part greater then return that
//if first part equal, check second part, return that
if ($regsA[1] != $regsB[1]){
return($regsA[1] > $regsB[1]);
else {
if ($regsA[2] != $regsB[2]){
return ($regsA[2] > $regsB[2]);
else {
if ($regsA[3] != $regsB[3]){
return ($regsA[3] > $regsB[3]);
if ($regsA[4] != $regsB[4]){
return ((“0.”.$regsA[4]) > (“0.”.$regsB[4]));
else {
if ($regsA[5] != $regsB[5]){
return ($regsA[5] > $regsB[5]);
else {
if ($regsA[6] != $regsB[6]){
return ($regsA[6] > $regsB[6]);
else {
if ($regsA[7] != $regsB[7]){
return ($regsA[7] > $regsB[7]);
else {
return ($regsA[8] > $regsB[8]);

[Photomedia Forum post by T.Neugebauer from Jan 17, 2012  ]

information retrieval: relevance, pertinence, precision and recall

The relevance of information in relation to some question was defined in the late 1950s when the Cranfield test was developed at the Cranfield College of Aeronautics . The two measures that were developed are precision and recall.


The extent to which information retrieved in a search of a library collection or other resource, such as an online catalog or bibliographic database, is judged by the user to be applicable to (“about”) the subject of the query. Relevance depends on the searcher’s subjective perception of the degree to which the document fulfills the information need, which may or may not have been
expressed fully or with precision in the search statement. Measures of the effectiveness of information retrieval, such as precision and recall, depend on the relevance of search results.

Compare with pertinence.

In information retrieval, the extent to which a document retrieved in response to a query actually satisfies the information need, depending on the user’s current state of knowledge–a narrower concept than relevance. Although a document may be relevant to the subject of the inquiry, it may already be known to the searcher, written in a language the user does not read, available in a format the reseacher is unable or unwilling to use, or unacceptable for some other reason.

In information retrieval, a measure of search effectiveness, expressed as the ratio of relevant records or documents retrieved from a database to the total number retrieved in response to the query;

Compare with recall.

recall In information retrieval, a measure of the effectiveness of a search, expressed as the ratio of the number of relevant records or documents retrieved in response to the query to the total number of relevant records or documents in the database;One of the main difficulties in using recall as a measure of search effectiveness is that it can be nearly impossible to determine the total number of relevant records in all but very small databases.

source: ODLIS: Online Dictionary for Library and Information Science


Fairthorne, Robert A. in “The Symmetries of Ignorance” distinguishes between two kinds of aboutness, extensional and intentional:

Robert Fairthorne writes: “The problem of helping those who are ignorant, in detail, of what people have said about things, is therefore solved by defining ‘aboutness’ in extension. That is by listing the things that are mentioned in a document. . . .” […]
(1) extensional “aboutness” takes into account the environment of the use and the production of a document (thus it is a relation, not an attribute);
and (2) intentional “aboutness,” which clearly cannot be determined from the study of the text alone: “It entails knowledge of how it is going to be used by what class of readers.”The Role of Classification in Subject Retrieval in the Future by Rolland-Thomas, Paule

[Photomedia Forum post by T.Neugebauer from Jan 13, 2007 ]

Access 2006 Conference in Ottawa

I recently participated in the Access 2006 Conference in Ottawa

Common touchstones at the conference include:* customized web applications and search interfaces
* open source software
* national and provincial consortiae initiatives
* information policy
* digital media
* library catalogue innovations
* end user searching behaviours
* metadata

source: what is Access?

Some notes from the CARL Preconference on Institutional Repositories

Benefits of institutional repositories include: impact, visibility, and reputation.

CARL Harvester, CARLCore is unqualified Dublin Core.
OAI-PMH metadata protocol = Deposit -> metadata generation -> aggregations -> end user
URIOpenURL vs. DOICrossref (proprietary)
International Federation of Library Associations and Institutions (IFLA) – search for institutional repositories

University of Toronto:
University of Toronto’s Knowledge Media Design Institute – virtual institute
Project Open Source | Open Access (

Open Access Examples:
Public Knowledge Project
Data Liberation Initiative

An online portal to full text anthropological resources, AnthroSource offers AAA members access to 40,661 articles in AAA journals, newsletters, bulletins, and monographs; a linked, searchable database containing past, present, and future AAA periodicals; centralized access to a wealth of other key anthropological resources, including text, sound, and video; and interactive services to foster communities of interest and practice throughout the discipline.


Bioline International – a not-for-profit electronic publishing service committed to providing open access to quality research journals published in developing countries
Journal of Medical Internet Research
National e-Science Centre (UK)

Examples from Europe:
University of Glasgow ePrints Service
Queensland University of Technology
CERN Document Server

Institutional Repository Software:
Fedora – Fez (web interface to Fedora) and other tools

notes from Access 2006

Canada and Ontario:
Canadian Initiative on Digital Libraries
Ontario Scholars Portal

Library Enterprise System vs. ILS
– refinement and knowledge discovery
Canadian Research Knowledge Network (CRKN)

Increase in cost, paying for publishing and access > Biomed Central

>PrestoSpace – AV Materials
>Building resources for Integrated Cultural Knowledge Services (BRICKS)
>TEL (European Library)

Lucene – indexing search engine, archives, multiple metadata (EAD, DC, Fulltext), good at merging indexes. Solr – open source search server based on Lucene. Example: National Adult Literacy Database.

Endeca – NCSU catalog (Endeca for faceted browse, relevance ranking).

Search comforts: spell (did you mean?), stemming, sort options
Search + browse: layered facets, filter across multiple dimensions, facet deselection, relevance, speed, locally managed, persistent parameters

Cocoon – XML publishing framework
Ruby on Rails – agile web development
LizardTech – for MrSID and JPEG 2000 images

Collex –

a set of tools designed to aid students and scholars working in networked archives and federated repositories of humanities materials: a sophisticated COLLections and EXhibits mechanism for the semantic web


University of Victoria -> backup catalog using PHP – Yaz

a tiny HTTP API for the few basic operations necessary to copy discrete, identified content from any kind of web application


XML Databases – alternative: SQL + Lucene

XML Catalogues / Library 2.0 – “an architecture of participation”
>eXtensible Catalog (XC) – an open-source online system that will unify access to traditional and digital library resources
>TalisKeystoneresourcestalk.talis.comdirectory.talis.comdevelopment networkProject Cenote
>Library Thing (beta)
>Library 2.0 Wiki

>LibX Firefox

Web services
xISBN service
Amazon APIAmazon Elastic Compute Cloud (Amazon EC2) – Limited Beta
Google API

> Service Oriented Architecture (SOA) – more enduring and flexible, reusable (sustainable?)
– BPEL (OASIS standard) for expression of complex processes. Active BPEL (Open Source), Active BPEL Designer (visual designer).
– services invoked with SOAP
– orchestration exposed with WSDL

> UK -> Structured Vocabularies for IR (thesauri, ontologies, etc.) > British Standard – BS8723
Controlled Vocabularies: LCSH, Rameau (Fr), SWD (de)
e-Framework for Education and Research – an initiative by the UK’s Joint Information Systems Committee (JISC) and Australia’s Department of Education, Science and Training (DEST)
Digital Library Federation – DLF Service Framework for Digital Libraries
NISO MetaSearch Initiative
NISO RP-2006 – Best Practices for Designing Web Services in the Library Context (PDF)
SOA in higher education
DELOS – Network of Excellence on Digital Libraries

Discussion lists:

>Bibliothek Hamburg

Book reference:
Putting Content Online: a practical guide for libraries” by Mark Jordan

[Photomedia Forum post by T.Neugebauer from Oct 18, 2006]

Nondeterministic Turing Machines

In theoretical computer science, there is a theorem which states that all nondeterministic Turing machines (NTM) have an equivalent deterministic Turing machine (DTM). NTMs differ from DTMs in that the former allow for the possibility of more than one next state from a given configuration.

If there is more than one next move, we do not specify which next move the machine makes, only that it chooses one such move.

source: Computability and Complexity Theory, Steven Homer & Alan Selman, p.31

The proof for the theorem that NTMs have equivalent DTMs is through construction: the DTM builds NTM’s computation tree and then performs a breadth-first search on this tree. I was never convinced by this proof. If you take time into consideration, and the fact that NTM’s computation tree approaches infinity in size due to the size of the option set from which it ‘chooses’ at each step, you get a search that takes the DTM forever (or almost forever) to complete (which, to borrow Douglas Bridges’ expression, “does not extend to an assurance that you will find the desired term before the end of the universe”). I remain unconvinced that NTMs are equivalent to DTMs.

[Photomedia Forum post by T.Neugebauer from Jun 20, 2006]

Ryszard Kapuściński, a poetic reporter of the human condition

Ryszard Kapuściński was a historian, writer and journalist. His reporting was both philosophical and poetic without sacrificing fact, the inventor of ‘literary reportage’. I’ve read his Heban(Ebony), Szachinszach (Shah of Shahs), Cesarz (Emperor). He specialized in Africa and Latin America and Cesarz (Emperor), the story of Haile Selassie, is his best known book. He did also write about the Soviet Union, the first part of his Imperium (First encounters 1939-1967) describes Kapuściński’s original voyage through Belarus, Siberia, Georgia, Armenia, Azerbeijan, Turkmenistan, Tajikistan, Kirghiz, and Uzbekhistan. Here is my translation of Kapuściński’s description of an encounter with Gulnara Gusein, a medical student and phytotherapist in Azerbeijan

People come to Gulnara with a paper from professor Gasanov. On the paper, the professor prescribed the name of a flower and the duration of smelling. The smelling is done sitting down, most often for ten minutes. Gulnara oversees so that everyone is smelling what they are supposed to, so that, for example, a sclerotic does not begin to smell rosemary. The flowers stand in rows in a glass house that is called a phytotherapy office, it is reminiscent of a greenhouse. Gulnara tells me to sit down and also smell something. Can I sense the scent? I don’t smell anything. Obviously – that is because a flower does not emit a scent all for itself. One has to touch the stem, and the flower can feel that someone is showing interest in it. And it starts to emit its aroma. Every stir the flower meets with aroma – it is naive and frivolous, it wants to be liked by everyone. Comrades, stir up the flowers! – Gulnara reminds the elders sitting in the study, who start to stir the stems as though they were shaking ants off of them.

I ask Gulnara, who is a medical student, if she believes, that a flower can cure a human being. Cure not psychologically, because this possibility has been substantiated, but cure physically, for example return elasticity to a calcifying cell. Gulnara smiles. She says only, that people from all over the world come to see her. She emphasizes: even from America. Professor Gasanov’s method – therapy using the scent of flowers – has already become well known.

I think that for Gulnara, like for me, the charm of this method is not only its aesthetic trait, but also its cheer and goodly wisdom. What is the professor supposed to do with an elder that carries seven crosses and forgets their date of birth? Of course, the professor could put them in a crowded hospital room, into the odor of chloroform and iodine. But what for? Is a twilight that smells of flowers not more beautiful than the twilight of chloroform? So when the professor sees someone, who has to look into their identity documents to give him their own date of birth, and complains, that his head is silting somehow, professor listens carefully, and then writes on the paper: “Rp.: Laurel leaves. Ten minutes a day. For three weeks.” And look, says Gulnara, crowds try to see the professor. The waiting list lasts for months.

source: translated from Polish, Imperium, 2001 edition, p 58-

While in Armenia, he recounts the biography of Soghomon Soghomonyan (Komitas), as it was told to him by the young composer Emina Aristakesjana.

1915, the beginning of the massacre of Armenians in Turkey. Until the times of Hitler, it was the greatest massacre in the history of the world, one and a half million Armenians died. Turkish soldiers dragged Komitas on a cliff from whence they were to execute him. At the last moment the daughter of the sultan of Istanbul saved him, his student. But he already saw the abyss and this disturbed his mind.

He was 45 then. Someone took him to Paris. He did not know that he is in Paris. He lived another 20 years in an insane asylum. He walked little, was silent, but looked on. Perhaps he saw those who came to visit him, they say that he stared at their faces.

When spoken to he did not respond.

They tried different things. They sat him down in front of an organ. He got up and left. They played records for him. He gave the impression that he did not hear. Someone placed on his lap the Armenian instrument, tar. He carefully put it away. Nobody knows for sure if he was ill. Perhaps he chose silence?

Maybe that was his freedom.
He did not die, but he was no longer alive.
He existed-in-non-existence in this hanging between life and death, in the lunatic purgatory. Those who visited him say that he was increasingly tired. He stooped, thinned, darkened. Sometimes he fidgeted his fingers on the table, in silence, because the table made no sound. He was calm, always serious.

He died in 1935: so after 20 years he fell into that abyss before which the daughter of the sultan of Istanbul saved him, his student.

source: translated from Polish, Imperium, 2001 edition, p 51-

Kapuściński died last Tuesday, January 23, 2007.

This man who witnessed 30 coups and revolutions and counted Che Guevara, Salvador Allende and Patrice Lumumba among his friends


In his “Travels with Herodotus,” due to be published in the United States this year, Kapuscinski offers tribute to the Greek historian he considered the world’s first great reporter.

In a 2003 speech, Kapuscinski explained Herodotus’ formula for successful journalism: First, be willing to submit to hard, painstaking travel to get information first hand. Then, be able to listen carefully and respectfully to people. Third, do your homework, be investigative and precise. Journalists must be “missionaries, translators and messengers.”

Retrieved from:  International Herald Tribune. “Kapuscinski, master of literature of fact ”

see also: NPR – audio of 1988 interview with Ryszard Kapuscinski

[Edited from Photomedia Forum post by T.Neugebauer from Jan 28, 2007   ]

Europeana – ideas, inspiration, culture is a collaboration between universities, research institutes and content providers. It was launched this year as a beta, and is scheduled to be available as a release in 2010.

The site includes a link to a prototype of the Europeana semantic search, as well as a functional beta Timeline navigator, communities and more.

Europeana links you to 4 million digital items including images, texts, sounds and videos from museums and galleries, archives, libraries and audio-visual collections. The list of organizations contributing content includes the Rijksmuseum in Amsterdam, the British Library in London and the Louvre in Paris.

[Edited from Photomedia Forum post by T.Neugebauer from Aug 07, 2009]

Komitas, a.k.a. Soghomon Soghomonyan

Some music by the great Armenian monk-composer Soghomon Soghomonyan (Komitas) can be found in the virtual museum of Komitas. Komitas is credited for bringing a renaissance to Armenian music through his collection and arrangement of over 3000 Armenian folk songs.

Gomidas Songs

Isabel Bayrakdarian was on CBC Radio today, presenting her new album Gomidas Songs .

The life of Father Gomidas is a powerful story of devotion and passion for his country, its people and its music — and it is one beautifully explored by Isabel Bayrakdarian and her husband, pianist and composer Serouj Kradijan, in a new CD called “Gomidas Songs.” THE_SUNDAY_EDITION, 2008 12 14

[Edited from Photomedia Forum post by T.Neugebauer from 2007-2008  ]