2013 in review

The WordPress.com stats helper monkeys prepared a 2013 annual report for this blog.

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 8,800 times in 2013. If it were a concert at Sydney Opera House, it would take about 3 sold-out performances for that many people to see it.

Click here to see the complete report.

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New Informatics Approach Combines Metabolic, Regulatory Networks to Elucidate Cells’ Activities

A new paper written by researchers from the Institute for Systems Biology describes a computational approach for studying regulatory activities in cells that relies on integrated networks of transcriptional and metabolic data.

The study, published in PLOS Computational Biology earlier this month, describes software called the Gene Expression and Metabolism Integrated for Network Inference (GEMINI) which uses an integrated model of network and metabolic data to explore growth phenotypes in Saccharomyces cerevisiae .

GEMINI builds on work from the same researchers published in 2010 in the Proceedings of the National Academy of Sciences. That paper describes the Probabilistic Regulation of Metabolism (PROM), which provides a mechanism for integrating transcriptional regulatory networks and metabolic networks in a single in silico model and using it to make predictions about phenotypes such as flux and growth rate.

While based on PROM, GEMINI is designed to tackle a slightly different question, as the PLOS Comp. Bio. paper explains. While PROM “solves the forward problem of combining disparate networks to predict phenotype” with GEMINI “we iteratively use PROM to aid in solving the more challenging inverse problem — guiding TRN structure prediction using the metabolic network and the emergent phenotype measurements,” the researchers wrote. “In doing so, our new method serves as a tool to refine the inferred TRN and improve the predictive power of the integrated network models.”

Nathan Price, ISB’s associate director and co-author on both papers, explained that while PROM uses the integrated network to try to predict what happens when transcription factors are deleted, GEMINI says “we don’t know what the gene regulatory network is perfectly so we are going to use the fact that we can link these two together to now look at where we make wrong predictions,” 

“GEMINI says, [for example], ‘I have a prediction that this transcription factor influences a gene that happens to code for a metabolic enzyme,'” Price said. “Because we can link these things together and make growth predictions, we can say, ‘When we knock out that transcription factor in yeast, does it have the decrease in growth rate that we predict because of this regulatory interaction.'”

The developers claim that theirs is the first approach that integrates regulatory and metabolic data in this way and use it to study cell’s activities. They write in PLOS Comp. Bio that it improves on previous strategies that have used primarily “proximal data such as gene co-expression and transcription factor binding” to reconstruct and study TRNs. While these methods, they said, can be used to quickly reconstruct TRNs, “the overwhelming combinatorics of possible networks limits identification of mechanistic regulatory interactions.”
Their findings, the researchers conclude, “suggest that a metabolic constraint-based approach can be successfully used to help reconstruct TRNs from high-throughput data, and highlights the potential of using a biochemically-detailed mechanistic framework to integrate and reconcile inconsistencies across different data-types.”
Metabolic networks are one of the better understood cellular systems, according to Price, making it the ideal starting point for studying at least those regulatory activities in which cell metabolism plays a role, such as growth rates.

“It’s hard to just look at a transcriptome and say [for example] if I knock out a transcription factor, that is going to lead to the death of this tuberculosis cell,” he said. “But as soon as you tie it on to metabolism, there are very … clear rules about what … leads to cell death in metabolism in a way that you don’t see directly in gene regulatory networks.”
For their next steps, Price and his colleague and co-author, Sriram Chandrasekaran, are trying to use GEMINI to study networks in cells other than yeast, such as human cell lines. He also said that they’re exploring ways to integrate it with network inference algorithms with an eye toward creating a “model-guided platform for synthetic biology.” A third potential application would be to use GEMINI to study regulatory-metabolic interactions associated with disease-specific cancers, as well as metabolic and neurodegenerative diseases, he said. 
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Bioinformatics Workshop on ‘Structural Bioinformatics’ at BISR, Jaipur, India

January 10-12, 2014 
Birla Institute of Scientific Research, Statue Circle, Jaipur, India 
[link] 

Bioinformatics Centre at Birla Institute of Scientific Research, Jaipur is organizing a three-day Bioinformatics workshop on “Structural Bioinformatics”. BISR is known for providing a high quality training in advance area of Biotechnology and Bioinformatics. 

This workshop will enable participants to learn tools & techniques that are being used to analyze biological structures i.e. proteins and DNA along with application in drug design. The workshop will feature morning lectures, demonstrations with evening hands-on session in Bioinformatics lab. 

The no. of participants is limited to 40 only. The participants of the course may be the UG/PG students, research scholars, faculty member and industry personnel with background in Biological Sciences and/or Information Technology. The workshop is self-contained and does not assume any special knowledge of the subject. 

REGISTRATION: 
Last date of registration is 1st January 2014. Application form and brochure may be downloaded from the website. For further details kindly visithttp://www.bisr.res.in or email to the convener at workshop.bisr[at]gmail.com.var gaJsHost = ((“https:” == document.location.protocol) ? “https://ssl.” : “http://www.”); document.write(unescape(“%3Cscript src='” + gaJsHost + “google-analytics.com/ga.js’ type=’text/javascript’%3E%3C/script%3E”)); var pageTracker = _gat._getTracker(“UA-2697320-3”); pageTracker._initData(); pageTracker._trackPageview();

Accelrys Acquires Qumas for $50M

Accelrys has bought Qumas, a provider of cloud-based and on-premise enterprise compliance software for regulatory and quality operations in regulated industries including the life sciences, for $50 million.
Accelrys said that the added intellectual property extends its informatics portfolio by providing document and process management compliance solutions that improve its ability to help customers reduce regulatory risks and quality costs, improve compliance, and increase operational efficiency across their product development lifecyles.

Operating from offices in Cork, Ireland and New Jersey, Qumas provides an electronic document management application with related research and development submission and QA documentation packages based on customer and industry requirements and best practices.
Its business process management applications include corrective action/preventive action, audit, change control, deviation, complaint, and more. For the last two decades, the company has been involved in integrating content, processes, people, and systems into enterprise compliance programs that eliminate the cost and complexity associated with managing paper-based, disparate or legacy document management applications.

As part of an integrated solution, Accelrys said that applications such as the Accelrys Electronic Lab Notebook, Accelrys Laboratory Information Management System, Accelrys Lab Execution System, and Accelrys Discoverant for Operational Intelligence will function as data sources and integration points for the compliance and quality business systems that Qumas’ solutions manage.
“Integrating QUMAS solutions into the Accelrys product portfolio will provide a single-vendor [scientific innovation lifecycle management] solution that is already in high demand for product lifecycle management into the critical compliance and quality management arena for science-based process industries,” Accelrys President and CEO Max Carnecchia, said in a statement.
It also enables Qumas to extend its customer base in other business areas currently served by Accelrys, Qumas CEO Kevin O’Leary added.

Under the terms of the agreement, in consideration for acquiring all of the outstanding capital stock of Qumas, Accelrys agreed to pay to the company’s shareholders a total of approximately $50 million in cash, subject to working capital and other adjustments. The transaction is expected to be neutral to Accelrys’ non-GAAP earnings per share for the year ending Dec. 31, 2013, with a $1 million to $2 million non-GAAP revenue contribution.

Qumas had revenues of $15.2 million for the year ended Dec. 31, 2012.
This is Accelrys’ second acquisition for the year. In January, the company bought Vialis, a systems integration firm headquartered in Liestal, Switzerland, for up to $10 million.
In its most recent financial report, Accelrys posted a 1 percent bump in third quarter revenues for a total of $40.9 million for the three months ended Sept 30, compared to $40.5 million for the same period a year ago.
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Bioinformatics Short Time Courses

Here are some bioinformatics courses, These are geared towards:


– Scientists, so they can think like a programmer and solve bottlenecks in data-based Biology
– Computer programmers, so they know how to solve bioinformatics problems for scientists
– Bioinformaticians, so they can advance their skills in newer application areas

Some of these courses include scripting and database management with Linux, Perl, R, Matlab and MySql, while others include learning to use software for analyzing data from Microarray, NGS, Metabolomics and Proteomics platforms. A course on High Performance Computing and Primer Design is also offered. A detailed roster of scheduled courses is available at:
http://www.bioinformatics.org/edu/calendar/view.php?view=upcoming

Additionally, through Bioinformatics.org, an instructor-led program in practical bioinformatics is being offered. The goal here is to provide attendees a broad overview of the bioinformatics landscape, while giving them hands-on experience with tools used in various application areas of bioinformatics such as NGS, Microarrays, Metabolomics and Proteomics. Details can be found at: http://www.bioinformatics.org/wiki/Educational_services#Trainer-Led_Program_in_Bioinformatics
 
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Senator Rand Paul (R-Ky.) Draws some inspiration from BioSaga Blog

var gaJsHost = ((“https:” == document.location.protocol) ? “https://ssl.” : “http://www.”); document.write(unescape(“%3Cscript src='” + gaJsHost + “google-analytics.com/ga.js’ type=’text/javascript’%3E%3C/script%3E”)); var pageTracker = _gat._getTracker(“UA-2697320-3”); pageTracker._initData(); pageTracker._trackPageview(); GATTACA has always been one of my favorites; every now and then I have used it as a reference in many of my posts, this one being the recent! Genome From Birth – Dawn of the GATTACA era!

This is what Senator Rand Paul (R-Ky.) says in his latest public address;

Speaking at a Liberty University event in Virginia, Senator Rand Paul (R-Ky.) warned that genetic testing could lead to eugenics à la the 1997 movie Gattaca, reports the Associated Press.
“In your lifetime, much of your potential — or lack thereof — can be known simply by swabbing the inside of your cheek,” Paul said. “Are we prepared to select out the imperfect among us?” He was campaigning in Virginia for gubernatorial candidate Ken Cuccinelli.

Other aspects of Paul’s speech referring to the dystopian movie, though, resembled the Wikipedia entry on the movie, Rachel Maddow pointed out on her show on Monday. USA Today notes that Paul has not responded to those accusations.

Paul added that he was not against science, noting that he is a physician, and he praised the decrease in childhood mortality rates and the increase in life expectancy during the past 100 years, according to the video at USA Today.

Illumina to Acquire NextBio, Integrate Firm into Enterprise Informatics Business

var gaJsHost = ((“https:” == document.location.protocol) ? “https://ssl.” : “http://www.”); document.write(unescape(“%3Cscript src='” + gaJsHost + “google-analytics.com/ga.js’ type=’text/javascript’%3E%3C/script%3E”)); var pageTracker = _gat._getTracker(“UA-2697320-3”); pageTracker._initData(); pageTracker._trackPageview(); Illumina today announced it signed a definitive agreement to acquire clinical software firm NextBio.

NextBio, based in Santa Clara, Calif., provides platforms to aggregate and analyze large amounts of phenotypic and genomic data for research and clinical applications. It currently has customers at more than 50 commercial entities and academic institutions.

By acquiring the firm, Illumina “will be able to offer customers enterprise-level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare,” according to a company statement.

NextBio’s platform allows customers to compare experimental data against existing data sets using a correlation engine, enabling them to discover new associations. It uses “highly scalable” software-as-a-service enterprise technology and is capable of analyzing petabytes of data.

Illumina plans to combine its BaseSpace cloud computing environment for next-generation sequencing data with NextBio’s platform for integrating patient data.

The acquisition is expected to close by the end of October. No financial terms were provided.

Illumina will integrate NextBio into its newly-formed Enterprise Informatics business and will retain NextBio’s co-founder Ilya Kupershmidt and Chief Technology Officer Satnam Alag.

a chronicle of life sciences & informatics