News

Craic has published a detailed tutorial on using Google's BERT language representation model to classify biomedical research papers.

This approach combines the large pre-trained dataset in BERT with fine-tuning using domain-specific set of Pubmed abstracts. The resulting model is able to distinguish between papers that describe therapeutic antibodies against human antigens from other papers with an accuracy of around 91%, much higher than other approaches using term frequencies, etc.

The tutorial and associated data preparation scripts can be found on GitHub.

Arduino Power provides an open-source hardware and software solution to managing the power for portable systems using Arduino microcontrollers.

The hardware links an Adafruit PowerBoost Shield and a Data Logging Shield to an Arduino, with software that monitors and logs battery voltage to an SD card.

The circuits and software are available on GitHub and are distributed freely under the MIT license.

Pi Power provides a hardware and software solution to managing the power sources for portable Raspberry Pi projects that works like many mobile phones.

It implements the functions that we have grown to expect on mobile phones:

• Power up / Power down by pushing a button
• Automatic charging when a USB power cord is connected
• A simple status showing how much battery life remains
• An alert when the battery is very low
• Safe shutdown when the battery runs out

The hardware links an Adafruit PowerBoost 1000C charger to the Pi and two background scripts monitor the battery and update the status LEDs.

Pi Power appears to be the first complete solution to powering portable Pi systems.

The circuits and software are available on GitHub and are distributed freely under the MIT license.

Our paper describing the genome of the nitrogen-fixing soil bacterium Azotobacter chroococcum has been published in the journal PLoS One.

Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

Robert L. Robson, Robert Jones, R. Moyra Robson, Ariel Schwartz, Toby H. Richardson

You can find the paper HERE

Rob Robson has worked on A.chroococcum since the 1980s, back when he was my Ph.D. supervisor. Working together on this project to sequence and characterize the entire genome has been an excellent way to mark his research career.

GenBank has released the genome sequence of the nitrogen fixing bacterium Azotobacter chroococcum and its six plasmids.

A.chroococcum NCIMB 8003 (ATCC 4412) is a free-living member of the gamma-proteobacteria used in studies of nitrogen fixation and hydrogen metabolism. This strain contains six plasmids.

The project has been a collaboration between Rob Jones (Craic), Rob and Moy Robson (Univ. Reading, UK) and Ariel Schwartz and Toby Richardson (Synthetic Genomics, USA).

Links to the Sequence data and other resources can be found at azotobacter.craic.com.

I am pleased to announce the launch of a web site for Lakou Lapè - a Haitian non-profit group working to reduce violence and conflict in the communities of that country.

I have been working with the group over the past year as it has taken shape to create a web site that describes their approach to reconciliation, dialogue and mutual respect that can help reduce the violence that plagues the impoverished neighborhoods of Haiti.

Working with the Glencree Centre for Peace and Reconcilliation in Ireland, Lakou Lapè is using the same approaches that helped bring peace to Northen Ireland. I am proud to have worked with my new friends in Haiti and an old friend from Glencree in building the site and communicating their message to a broader audience.

UPDATE 2016 - The Lakou Lape site is now managed by another group

Craic has launched Web Apprentice - providing tutorials on web technologies, HTML5, JavaScript libraries and APIs.

The range of web services and libraries that you can include in your web sites is just incredible right now - from maps and charts to translation and speech recognition.

But getting started with a new technology can be a challenge and many online resources are confusing and sometimes out of date.

Web Apprentice is a site that offers clear tutorials on all kinds of web technologies. Eash has a clear description and code walk-through, a self-contained live demo and code that you can use to build your own pages.

The goal of the site is to introduce web designers and developers, at all levels, to the exciting new technologies that are available and to encourage them to experiment with them.

Craic has launched a new Online Language Learning service called Vocabrio

Vocabrio uses cutting edge Web Technologies to help you improve vocabulary in a target language. Web Audio and Speech Synthesis are used to pronounce any word that you choose. You can test your own pronunciation through the use of advanced Speech Recognition.

Rather than rely on boring textbooks for vocabulary, you can install the Vocabrio bookmark in your browser then go to any web site in your language. When you click on words that you don't understand, Vocabrio will translate them and add them to your custom dictionary.

You can challenge yourself with quizzes based on your dictionary to reinforce the vocabulary that is relevant to you.

Vocabrio is in Beta test and currently it is free to use. After we work any bugs out of the service then it will change into a paid subscription service.

Learn more and sign up for your account at Vocabrio

Craic has published a tutorial on remote server calls with JSON and JSONP from JQuery with clear code examples.

JSONP is a way to get around the Same Origin Policy restriction when a script in one domain wants to fetch JSON data from a server in a different domain. It can be a very useful approach when connecting multiple remote data services.

The example code is available on our Github Account and a Live Version can be found at http://json-jsonp-tutorial.craic.com

Genetic Engineering and Biotechnology News has published an article by Robert Jones that shows that many biotech and pharma companies are still using old versions of web browsers that are not compatible with new HTML5 web technologies.

Examination of server logs for a biotechnology database shows that 45% of all users, from a range of companies, are using browsers that are not able to use all the features of HTML5, which is the current version of the core web technologies. Among users of Internet Explorer, the default browser in Microsoft installations, 85% of users are using browsers that are 2 or more generations old.

IT in Biotech companies tends to be inherently conservative for reasons of security, budget and regulatory compliance. But this approach will result in researchers being unable to use the latest tools, especially in terms of data visualization. As an industry we need to devote both effort and budget to ensure computing resources remain current.

Craic has released a new tool to help count features in images. This can be used in a range of applications such as counting buildings in satellite images, bacterial colonies and cell types in histology images.

The tool can be accessed live at http://counter.craic.com. The code is made freely available under the MIT license and can be found on our Github site.

Craic has released experimental code to help identify temporary shelters in slums and refugee camps using satellite images from Google Maps.

The code is freely available for download and further development at our Github repository. A brief report on the work, with examples of it application to the slums in Port-au-Prince, Haiti, can be found HERE.

A number of areas of data analysis, such as satellite image analysis, are dominated by sophisticated algorithms, intensive computation and, in some cases, limited access to raw data.

We are interested in how simple, approximate methods can be used to extend the application of these technologies. While simple approaches will clearly not match the accuracy and resolution of complex methods, they can, by nature of their simplicity, be implemented and deployed more easily and hence more widely.

The October 2012 issue of Clinical Infectious Diseases includes a paper on the etiology of diarrhea in patients in a pediatric emergency department.

Diarrhea etiology in a pediatric emergency department: a case control study.

Craic built and operated the data management system for this case control study and Dr. Robert Jones is an author on the paper.

Our Tech Tips blog just hit two milestones in the same week - 200 posts and 100,000 total page views

Craic Computing Tech Tips is a blog where we post snippets of code, workarounds and software tips that we think might be of interest to others.

It has been running since 2007 and currently averages 4,600 page views per month from around the world.

We have built our business using Open Source software and rely on the advice of many other developers on the Web. Tech Tips is one of the ways in which we can return the favor and pass on our experiences. It is rewarding to see that this effort is helping so many other users.

Craic announces the release of a new programming utility called logit that helps record specific Unix commands along with comments to a log file.

Logit was developed to help record important steps during the analysis of bioinformatics datasets in a more efficient manner than cutting and pasting text from the terminal. In addition it allows the user to describe the steps from the command line without having to switch to a separate editor.

The tool was developed to be completely general and should prove useful to anyone using Unix command line tools for data analysis tasks.

logit is distributed freely under the MIT software license and is available on our github account.

Where possible, in our work we try to contribute to the software and informatics communities by making Software and Technical Advice freely available alongside the proprietary work we perform for our clients.

Craic announces the launch of Tabs - a New and Comprehensive database on Therapeutic Antibodies in development by biotechnology companies.

Using a combination of advanced data mining and expert manual curation, Tabs represents the most comprehensive resource on therapeutic antibodies developed thus far.

Antibody records in the database are linked to a range of associated data, including Antigens, Companies, Conditions/Indications, Clinical Trials, Papers, Patents and more. Importantly, the database tracks the synonyms that identify individual Antibodies, avoiding duplication and ambiguity in your own searches.

Users can browse the database and search using a wide range of criteria. They can define their own Sets of antibodies and download tables into Excel and citations into common Reference Management software. Email notification will alert users whenever relevant new data are added.

Your Business Development staff can see the status of competing Abs in development and your R&D staff can see relevant papers and patents directly, saving you hours of time searching through separate databases.

As of June 1, 2011, Tabs contains data on more than 950 antibodies, more than 400 Antigens, and more than 300 Companies.

Tabs is available as a web based subscription service and offers cost effective access to the latest developments in this fast moving field. You can find out more about the service and sign up for a Free 30 day trial at http://tabs.craic.com.

Craic has released an open-source jQuery plugin for tandem select menus in HTML forms.

Most of the tools and databases that we develop for our clients involve web interfaces. The JavaScript language and the jQuery library play an essential role in web development at Craic. Our work leverages the contributions of many developers in the open source community and, as part of that community, we feel that it is important to contribute to it.

Today Craic has released a new jQuery Plugin that makes it easier to create complex select menus in HTML forms.

A standard HTML multiple Select menu allows the user to select multiple options using Ctrl/Cmd-Click. But when the list of options is long, requiring the user to scroll, it becomes cumbersome and prone to errors.

An effective solution is to use two select menus in tandem, with buttons allowing options to be swapped between the two.

Tandem Select implements this as a jQuery Plugin that is simple to set up and easy to customize.

More information and demo pages for the plugin can be found HERE and the software can be downloaded from HERE.

Craic has released software that provides Tooltip Help for Rails 3 Web Applications.

Most of the web application development at Craic Computing uses Ruby on Rails, one of the leading open source web application frameworks. In doing so we gain tremendous benefit from the work of many developers in the Rails community who contribute tools and libraries to the project.

So we are especially pleased to announce that we have contributed our first Ruby Gem to the project. Simple Tooltip is a package of software that makes it very easy to add so-called Tooltip Help to web pages in a Rails application. Within the Ruby and Rails community these packages are called 'gems'.

Simple Tooltip allows developers to add online help to their pages which can use the rich formatting features of HTML. Users will see small help icons on their pages and clicking on, or hovering above, these will bring up popup windows that contain the help content.

An important feature of Simple Tooltip is that any given help item can occur in more than one language and the software will show that which is most appropriate to the user.

To try out Simple Tooltip, go to the Demo Site and to learn more about the software go to the project page on GitHub and RubyGems.org.

Craic has released PATSY - a novel web service that reformats US patents in a way that makes them easier to read.

The text of patents is extremely difficult to read. The language used is can be verbose and arcane. Patents typically contain long lists of terms that enumerate all possible variants of each component within an invention. Compounding this is the narrow two column format chosen by the USPTO with which to print these documents.

The end result is text that almost guarantees frustration, eyestrain and headaches. PATSY is a novel web application that aims to change this.

You enter a US patent number, or publication number, into PATSY. The software fetches the document from the USPTO web site and reformats in several ways, displaying the resulting page in your web browser. Paragraphs are split into separate sentences. Long sentences are split are punctuation into multiple lines. In addition, references to other patents are made into hyperlinks to their respective office web sites, or to PATSY directly in the case of US patents. Key phrases, such as 'SEQ ID NO' are highlighted and certain types of journal references are given links to the NIH PubMed site, allowing quick access to the underlying publications.

PATSY is an experiment and has a few limitations. It only works with US patents at the moment and some features are focused on biotechnology patents. The service is free to use so please try it out and see if it helps you with your work - PATSY.

Craic has released Raphaël Live, an interactive tool for exploring the Raphaël Vector Graphics JavaScript Library, developed by Dmitry Baranovskiy.

Raphaël makes it easy to create complex vector graphics in JavaScript in a way that is compatible with modern web browsers. Craic has created Raphaël Live as an interactive tool for learning how to use this library.

By combining Raphaël, jQuery and the CodeMirror in-browser code editor, Raphaël Live makes it easy to try out code examples.

In addition, the tool provides links to a series of tutorial examples that demonstrate the major components of Raphaël. Clicking on a link loads the code into the editor and displays the results. Users can modify the code and re-run it to see how different attributes and parameters affect the result. In this way you can get up to speed with this important library in no time.

The code for Raphaël Live is available on GitHub and is freely distributed under the MIT license.

Craic has released a Ruby binding for the lookup3.c code for generating 32-bit hashes.

This useful C library was developed by Bob Jenkins http://burtleburtle.net/bob/hash.

The Ruby code can be found in the Craic account on Github and is freely distributed under the MIT open source license.

The Journal of Infectious Diseases has published a study on risk factors for bacterial enteric infection in children that was performed in Washington State. Dr. Robert Jones is one of the authors of this paper.

Most studies prior to this have dealt with specific outbreaks of bacterias such as Salmonella or E.coli, but these represent only 10% of all such infections.

This study sought to identify risk factors for the much larger set of sporadic infections. An editorial in the same issue of the journal discusses the significance of this study.

Craic Computing was part of the consortium of groups involved in the study and developed the data management tools that supported it.

The findings of a study on Synthetic Genomics: Risks and Benefits for Science and Society have been published, including a paper on Sequence Screening by Dr. Robert Jones of Craic Computing.

The study was conducted in 2005 through 2007 by policy experts from the J. Craig Venter Institute, MIT and the CSIS, funded by the Sloan Foundation.

Dr. Robert Jones was asked to contribute to that study and prepare a background paper on the use of Sequence Screening as a way to detect misuse of this technology.

Craic Computing has completed an independent investigation into the source of abusive messages, sent to Usenet groups, relating to members of the US Chess Federation.

The primary technical conclusion is in agreement with that of a previous report from a USCF member.

The book 'Internet Forensics' by Robert Jones was published by O'Reilly Media today.

This book describes a wide range of techniques for tracking down the sites and servers behind phishing scams, spam and other forms of Internet fraud.