http://www.lifescisoft.com/blog/ Sun, 20 May 2012 08:11:18 +0000 Zend_Feed http://blogs.law.harvard.edu/tech/rss http://www.lifescisoft.com/blog/frozen-sample-management-freezerpro/
Part of what we're trying to do here at LifeSciSoft is make scientists aware of the software that's out there to help them perform their research more efficiently and effectively, as too often good software goes unnoticed. FreezerPro is a great example. Made by a small company (RURO), FreezerPro is something that many labs have wished to exist, not knowing that it already does!

FreezerPro is a fast, easy, reliable and secure web-based application which enables users to know precisely where a frozen sample is located even before opening the freezer door. Researchers find their sample quickly, retrieve it from the freezer and get back to their research. No frozen hands, and no rise in temperature among samples that are close to the front of the freezer because the door is left open while people rummage through it. FreezerPro can provide automatic alerts when there are a low number of sample aliquots, as sample expiration date approaches, when sample volume is low, or when freeze-thaw count is above a threshold (which means its great for frozen reagents and antibodies as well as collected samples). It's also GLP and GMP compliant for those of you in regulated environments.

Go ahead and check it out: FreezerPro on LifeSciSoft.

If that doesn't quite do the trick for you, feel free to explore our other sample management software.]]> Thu, 17 May 2012 21:39:17 +0000 http://www.lifescisoft.com/blog/agilent-toxicology-software-genespring/
Agilent's contribution will comprise the development of new software for toxicology data management, data analysis and data visualization. The novel software will be built using Agilent's GeneSpring multi-omics analysis platform.

For more information:
Press release from Agilent
Toxicology software on LifeSciSoft
Software from Agilent on LifeSciSoft]]> Thu, 17 May 2012 21:12:25 +0000 http://www.lifescisoft.com/blog/omicsoft-rna-seq-alignment-tool/ a study in the advance access edition of Bioinformatics about their Omisoft Sequence Aligner (OSA), a tool for RNA-Seq alignment. To keep it short and sweet, I'll jump right to the point.

OSA was benchmarked against TopHat v1.3.3 and v1.4.0, RUM v1.10 and SOAPsplice v1.8. To generate simulated data, they used the BEER pipeline to simulate "12 sets of 10 million pairs of paired-end RNA-Seq reads with three independent simulations at each of four different error rates (0%, 0.5%, 1% and 2%)". TopHat performed very well, reducing run time 4-10 fold and handling RNA-Seq data with higher error rates without as much of a decrease in performance. It had higher sensitivity than TopHat while having fewer false positives than SOAPspice and RUM.

OSA is free to academic users and can be downloaded here: http://omicsoft.com/osa. Go get it and start aligning those transcriptomes!

Related software:
Transcriptomics software on LifeSciSoft
Sequencing software on LifeSciSoft]]> Thu, 17 May 2012 20:44:51 +0000 http://www.lifescisoft.com/blog/acd-labs-releases-spectrus-workbooks/
Spectrus Workbooks is actually a portfolio of technique-specific software for spectroscopy and separations, delivering advanced data analysis and management to users desktops. The individual workbooks are being released throughout 2012, and ultimately will comprise of ACD/Spectrus Workbooks for NMR, Mass Spec, optical spectroscopy, chromatography, and more.

Additional information:
Press release from ACD Labs
Spectroscopy software on LifeSciSoft
Cheminformatics software on LifeSciSoft
Knowledge management software on LifeSciSoft]]> Tue, 15 May 2012 23:20:01 +0000 http://www.lifescisoft.com/blog/bwt-genomic-data-compression/
The team has developed a novel BWT algorithm that allows "human genome scale data to be computed on very moderate hardware." The new algorithm also improves data compression, compressing genomic data to a size 4-times smaller than standard BWT-based compression. Not too shabby.

They discuss the results in an article in Bioinformatics.

Related software:
Genomics software on LifeSciSoft
Data management software on LifeSciSoft]]> Tue, 15 May 2012 16:43:41 +0000 http://www.lifescisoft.com/blog/informatics-costs/ recent article in GEN makes the argument that as sequencing costs fall, the informatics costs of analyzing and managing all of that data are actually going to increase on a per-genome basis. Although, as Daniel MacArthur points out in the Genomes Unzipped blog, the argument is based on some wacky assumptions and alarmism over the costs of genomics data analysis are largely unfounded.

I won't steal Daniel's thunder, so I suggest reading his article. It's well worth the few minutes of your time that it'll take to read.

Related software:
Genomics software on LifeSciSoft
Bioinformatics software on LifeSciSoft ]]> Tue, 15 May 2012 16:12:30 +0000 http://www.lifescisoft.com/blog/new-tech-choice-behavior/
The FOCOM project will have multiple focuses. One will be the development of a virtual supermarket, in which the test consumer's physiology, behavior, and brain responses are tracked. FOCOM will also focus on the development of technologies to analyze the brain during eating.

To learn more about the FOCOM project, view the press release from Noldus Information Technology

Related information:
Behavioral software on LifeSciSoft]]> Tue, 15 May 2012 15:51:04 +0000 http://www.lifescisoft.com/blog/snp-primers-snpcheck/ recommendation of @archivist84, we decided to give a look at SNPCheck from the National Genetics Reference Laboratory at the University of Manchester. As was told to us, SNPCheck is "great for finding those pesky SNPs in your primers."

SNPCheck is exactly what it sounds like - a tool for checking for SNPs, specifically in predicted PCR primer binding sites. The tool can be used free to perform single batch checks, but it is also available for a £170 per year laboratory subscription which allows running up to 500 primer pairs at once and saving both primers and results. Seems to be a very worthwhile investment for labs doing a lot of PCR.

For more information on SNPCheck, or to check for SNPs in a single primer pair, you can go to the SNPCheck website.

Related information:
Molecular biology software on LifeSciSoft
Genetics software on LifeSciSoft]]> Tue, 15 May 2012 15:25:27 +0000 http://www.lifescisoft.com/blog/genomics-software-wins-awards/
In New Zealand, Biomatters has won the Microsoft Hi-Tech Emerging Company Award at the 2012 NZ Hi-Tech Awards. We met some of the Biomatters guys at Bio-IT World a few weeks back and saw the Geneious software first hand so it comes as no surprise to us that it would be winning awards - it's a great genomic analysis platform.

Although not wrapped up yet, Genalice has been nominated for the National ICT Innovation Award 2012 in the Netherlands for their clinical genomics data analysis platform. I know Bert from Genalice and will be rooting them on to win! You can read about their nomination in this press release.

Related software:
Genomics software on LifeSciSoft]]> Fri, 11 May 2012 19:07:09 +0000 http://www.lifescisoft.com/blog/definiens-tissue-studio-in-situ-hybridization-analysis/
For more information:
News release from Definiens
Tissue Studio on LifeSciSoft
Other Definiens software on LifeSciSoft
Life science imaging software on LifeSciSoft]]> Thu, 10 May 2012 18:40:38 +0000 http://www.lifescisoft.com/blog/simulations-plus-may-2012-conferences/
May 12 - Bioavailability and Bioequivalence: The Language of Drug Product Quality at the Chinese University of Hong Kong. Simulations Plus will be exhibiting and giving a following talk.

May 13-17 - RDD (Respiratory Drug Delivery) 2012 in Phoenix, Arizona. Simulations Plus will be exhibiting

May 20-24 - 6th SETAC World Congress 2012 and 22nd European Annual Meeting in Berlin, Germany. Simulations Plus will be exhibiting in booth #17

May 21-23 - AAPS 2012 National Biotechnology Conference in San Diego, CA. Simulations Plus will be exhibiting

May 21-23 - The Introductory GastroPlus Simulation and Modeling Workshop at the Parkyard Hotel in Shanghai, China

May 24-25 - APSTJ Annual Meeting at the Kobe International Conference Center in Kobe, Japan. Simulations Plus will be attending and presenting a poster.

Related information:
Software by Simulations Plus on LifeSciSoft
Pharmacology software on LifeSciSoft
Toxicology software on LifeSciSoft]]> Thu, 10 May 2012 18:12:59 +0000 http://www.lifescisoft.com/blog/battle-for-lab-it-eln/
It's a good article, and well worth the read. You can find it here.

Related information:
ELNs on LifeSciSoft
LIMS on LifeSciSoft]]> Thu, 10 May 2012 17:41:51 +0000 http://www.lifescisoft.com/blog/perkinelmer-search-genius-microsoft-sharepoint/
SearchGenius will allow both text and structure searches of data stored using Microsoft SharePoint or PerkinElmer's own E-Notebook, or for general internet searches (although structure searches are not enabled for internet searches). Results can be saved, annotated, and shared to allow easy retrieval and collaboration.

Additional SearchGenius features include:
• Easily created hyperlinks to interesting content
• Access from the SharePoint framework directly or from PerkinElmer’s E-Notebook
• Complete integration into the SharePoint 2010 FAST framework, avoiding additional IT overhead

For more information:
Press release from PerkinElmer
Software from PerkinElmer on LifeSciSoft
Data mining software on LifeSciSoft]]> Tue, 08 May 2012 14:51:07 +0000 http://www.lifescisoft.com/blog/life-science-software-events-12-05-07/
• Qlucore will be in Amsterdam from the 7th through the 9th at the 2nd European Association for Cancer Research (EACR) / Organisation for European Cancer Institutes (OECI) joint training course on molecular pathology in cancer, demonstrating their Omics Explorer software. If you have high-content omics data, stop by and take a look! More info.
• Noldus Information Technology will be at the Belgian Association for Psychological Sciences conference on the 10th and 11th, exhibiting their suite of behavioral research software. More info.
• Accelrys will be hosting its 2012 Accelrys User Group Meeting for Life Sciences from May 7th through May 9th. The meeting will be co-located with the 2012 International Meeting on Automated Compliance Systems (IMACS) at the Boston Marriott Long Wharf Hotel in Boston, MA. The Accelrys user group meeting will feature demonstrations, presentations, plenty of Q&A, and the first ever "usability lab." More info.
Related links:
Omics software on LifeSciSoft
Behavioral research software on LifeSciSoft
http://www.lifescisoft.com/blog/diagnosing-malaria-with-life-science-games/ protein folding or deciphering the connectome of the retina then perhaps it's time to move on from simple crowdsourced science games to crowdsourced diagnostics games! Well you're in luck... The Ozcan lab at UCLA have developed a game that crowdsources the diagnosis of malaria.

Malaria can be diagnosed through standard light microscopic imaging of red blood cells and further analysis of their morphology. This is a process that is often simply done by eye prior to further tests. To try to make such diagnoses cheaper, faster, and more efficient, the Ozcan lab created a game that asks users to differentiate normal red blood cells from infected red blood cells (after providing some guidance, of course). While the amateurs are far from perfect, by pooling the answers submitted by many people they actually achieve a result that is quite accurate. How accurate? Within 1.25% of that of trained medical professionals. It's incredible was life science software can be built to do.

You can learn more about the game, play it, and read the lab's accepted submission to PLoS ONE about it on their BioGames website.

More life science software on LifeSciSoft.]]> Thu, 03 May 2012 19:24:04 +0000 http://www.lifescisoft.com/blog/is-big-data-too-big/ too big. The article discusses the problem of the production of omics data increasing far faster than computing power, how compression is and isn't a solution, and the need for improved algorithms.

It's a good article, so I don't want to steal it's thunder. I'll just let you read it here.

Related topics:
Omics software on LifeSciSoft
Genomics software on LifeSciSoft]]> Tue, 01 May 2012 14:38:02 +0000 http://www.lifescisoft.com/blog/biobase-updates-explain-database/
Related information:
Life science databases on LifeSciSoft]]> Tue, 01 May 2012 14:12:39 +0000 http://www.lifescisoft.com/blog/textco-biosoftware-gene-inspector-20/
To celebrate the release, Textco is offering special discounts on Gene Inspector for both upgrades and new purchases.

For more information:
Press release from Textco BioSoftware
Gene Inspector on LifeSciSoft
Sequencing software on LifeSciSoft ]]> Tue, 01 May 2012 13:58:32 +0000 http://www.lifescisoft.com/blog/lims-eln-fine-line/ LIMS (laboratory information management systems) and ELNs (electronic laboratory notebooks) may very well be on a crash course. He argues that the audiences that the two were originally meant to serve, once very distinct, are blurring and blending and will eventually become one. Why? The same thing that makes the world go 'round: money.

Potter argues that the costs of having two systems and integrating them is simply too great and, ultimately, unnecessary if you could have one system that served both purposes. This is causing a blurring of the scope of either class of product, with many ELNs coming with features that would traditionally be within the realm of LIMS and vice versa.

Many companies are already combining offerings. Potter mentions that Starlims has an offering combining the functionality of an ELN, a LIMS, and an SDMS (scientific data management system). AgileBio is another that comes to mind with its LabCollector suite. There are certainly others.

Potter closes by saying this collision of galaxies will be a good thing, with the hybridization of ELN and LIMS creating efficiencies and new capabilities that were not previously available. We second that thought.

Still, I think his viewpoint is biased towards industry. I don't think the good old ELN will be going anywhere anytime soon, and indeed light LIMS or SDMS may not either, thanks to our friends in academia whose needs are a good deal simpler.

You can read the full post here: LIMS & ELN: A Collision Course]]> Mon, 30 Apr 2012 18:48:42 +0000 http://www.lifescisoft.com/blog/new-program-short-tandem-repeats/
lobSTR, collaboratively developed by scientists at MIT, Whitehead, and Tel Aviv University, is an algorithm that is many times faster and more effective at profiling STR loci. It also addresses biased sampling of STR alleles that results from gapped alignment mapping of STRs, which is how previous bioinformatic tools treated them. lobSTR is capable of accepting raw sequencing reads and provides users with the genotyping results.

For more information:
Paper about lobSTR in Genome Research
More genomics software on LifeSciSoft]]> Mon, 30 Apr 2012 15:56:15 +0000 http://www.lifescisoft.com/blog/simulations-plus-releases-gastroplus-80/
• Increased execution speed
• Use of the PBPK (physiologically based pharmacokinetics) model to simulate both inhibition and induction of transporters and enzymes in any tissue
• Enhanced modeling of drug absorption and distribution for ocular and pulmonary delivery
• Ability to specify dissolution rates as function of pH
• Enhanced PDPlus™ module for building pharmacodynamics (drug effect) models and predicting pharmacodynamic effects for new doses and dosage forms
• Addition of a paracellular permeability model that accounts for movement of drug between the epithelial cells lining the intestinal wall as well as drug transport into and through the intestinal epithelial cells
• An expanded library of animal physiologies
• "Sanity checks" to prevent users from running simulations with inputs that appear to be inconsistent

More information can be found here:
Press release from Simulations Plus
GastroPlus on LifeSciSoft
Pharmacology software on LifeSciSoft ]]> Sat, 28 Apr 2012 16:11:29 +0000 http://www.lifescisoft.com/blog/idbs-thomson-reuters-integrate-e-workbook-suite-cortellis/ SM, delivered through the Cortellis Targets API.

This joint solution from IDBS and Thomson Reuters will improve access to information useful to life science researchers in areas such as pharmacology, target identification and validation, and biomarker discovery. IDBS E-WorkBook customers will be able to access the Thomson Reuters data from the ScienceLink feature in the E-WorkBook ELN.

Additional information:
Press release from IDBS
Data management software on LifeSciSoft
Electronic Laboratory Notebooks on LifeSciSoft]]> Fri, 27 Apr 2012 19:42:08 +0000 http://www.lifescisoft.com/blog/illumina-releases-basespace-apps/
The apps store includes a public API allowing any interested developer to create apps for the BaseSpace platform. A host of commercial developers were also announced as development partners upon launch. These included Omixon, Strand Life Sciences, Knome, GenoLogics Life Sciences, Golden Helix, Ingenuity Systems, vBiomax Informatics, and Integromics among others.

Illumina also released its new iSAAC genome alignment software today. According to Illumina, iSAAC can map sequencing reads up to 10 times faster than previous alignment software.

For more information:
Press release from Illumina
Genomics Software on LifeSciSoft]]> Fri, 27 Apr 2012 14:49:53 +0000 http://www.lifescisoft.com/blog/definiens-digital-pathology-webinars/ More info from Definiens Imaging Software on LifeSciSoft]]> Tue, 24 Apr 2012 15:07:56 +0000 http://www.lifescisoft.com/blog/geneious-pro-56-released/ we covered the release of Geneious 5.6 Beta last month). From the read of the announcement, it seems like there aren't many surprises. The features that Biomatters highlighted in the beta version all made it to the full release.

But, now you can update your Geneious Pro software to the latest version without fear of bugs.

More info:
Notice from Geneious
Genomics Software on LifeSciSoft]]> Tue, 24 Apr 2012 14:56:09 +0000 http://www.lifescisoft.com/blog/nextbio-clinical-translational-medicine/
Similar to NextBio Research, which aggregates genomic and other omic research data, NextBio Clinical will act as an aggregator of clinical omic data. The goal, according to NextBio, is to allow for earlier application of clinical data in R&D.

Interested in learning more about NextBio Clinical? For those of you attending Bio-IT World tomorrow, Ilya Kupershmidt, Co-founder and VP of Products at NextBio, will be discussing the new platform in a talk at 3pm.

Relevant links:
Press release from NextBio
Omics software on LifeSciSoft
Genomics software on LifeSciSoft
Clinical research software on LifeSciSoft]]> Tue, 24 Apr 2012 12:59:35 +0000 http://www.lifescisoft.com/blog/eln-technologies-ipad-cerf-eln/
If you'll be at Bio-IT World, you can check out the new CERF for iPad at the CERF Booth, #318. In what is certainly one of the more appropriate contest prizes, they'll also be giving away an iPad.

Additional information:

Press release from ELN Technologies / Rescentris
More information about CERF on LifeSciSoft
Electronic laboratory notebooks on LifeSciSoft]]> Fri, 20 Apr 2012 16:19:02 +0000 http://www.lifescisoft.com/blog/lifescisoft-bioit-world/
If you'd like to meet up with us, drop us a line. Of course, we'd be especially happy to hear from more life science software companies!

Other awesome software-y goodness:
Life science software on LifeSciSoft. ]]> Fri, 20 Apr 2012 14:52:26 +0000 http://www.lifescisoft.com/blog/nonlinear-dynamics-conference-schedule/
• Experimental Biology 2012, April 21-25, San Diego, CA
• 103rd AOCS Annual Meeting & Expo, 29th April - 2nd May 2012, Long Beach, California, US
• AOHUPO 6th Congress, 5th – 7th May 2012, Beijing, China
• 60th ASMS Conference on Mass Spectrometry and Allied Topics, 20th – 24th May 2012, Vancouver, BC, Canada
• 6e Journées Scientifiques du Réseau Français Métabolomique et Fluxomique. 21st – 22nd May 2012, Nantes, France

You can see Nonlinear Dynamics full conference schedule here: Nonlinear Dynamics conference schedule

Software information:
Proteomics software on LifeSciSoft
Metabolomics software on LifeSciSoft]]> Fri, 20 Apr 2012 14:39:16 +0000 http://www.lifescisoft.com/blog/simulations-plus-admet-predictor-60/
MedChem Designer™ molecular drawing software from Simulations Plus is now integrated into ADMET Predictor. Improvements have been made to the GUI. Data visualization and export capabilities have been improved and expanded. Perhaps most importantly, new predictive models have been added for metabolism and toxicity.

ADMET Predictor™ is used for QSAR modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances.

For more information:
Press release from Simulations Plus
More info on ADMET Predictor
Pharmacology software on LifeSciSoft
Toxicology software on LifeSciSoft]]> Thu, 19 Apr 2012 20:52:50 +0000 http://www.lifescisoft.com/blog/clc-bio-convey-computer/
From the sound of it, we can expect to see more collaborations between CLC and Convey in the future.

You can read more in the press release from CLC bio.

Related software:
Genomics software on LifeSciSoft]]> Thu, 19 Apr 2012 15:15:15 +0000 http://www.lifescisoft.com/blog/agilent-gel-permeation-chromatography-size-exclusion-chromatography-software/
The new new GPC/SEC software is built on the Agilent OpenLAB framework and will share the look and feel of Agilent's OpenLAB CDS LC software. Agilent GPC/SEC software supports control and data collection from all instrumentation that supports RC.NET driver technology. This includes many Agilent systems and some non-Agilent systems.

More information:
Press release from Agilent
Spectroscopy software on LifeSciSoft]]> Thu, 19 Apr 2012 15:02:58 +0000 http://www.lifescisoft.com/blog/agilebio-protein-tracking-system-labcollector-lims/
AgileBio's Protein Tracking System is completely integrated with LabCollector. It is aimed at any protein production facilities.

More info:
Press release from AgileBio
LIMS on LifeSciSoft
Details of LabCollector LIMS]]> Wed, 18 Apr 2012 13:29:13 +0000 http://www.lifescisoft.com/blog/more-open-source-network-analysis/
We wrote about a week ago about an open source visualization software called Gephi and raved about how good it looks. It has company.

Cytoscape is another open source network analysis software program and looks every bit as awesome. Both are, at heart, network data visualization software. They won't wow you with analysis, at least not out of the box, but they try to get you to analyze your own data through an improved understanding of it. They both have a reasonably large database of plugins. Sure, Gehpi is still technically in beta while Cytoscape is up to version 2.8, but that doesn't necessarily mean anything. Gephi seems to handle large data sets better, although Cytoscape has an easily implementable hack to get it to run larger sets well also.

Where Cytoscape wins, IMO, is that it is targeted to the life science community. This means that the plugins are much more life science-friendly. For example, there's a BLAST plugin. There are two plugins for omics data. There's a plugin to do academic literature searches. The list continues.

I'm not here to choose a winner, and I haven't seen enough of either to say which is better. All I can say is that they're both really cool.

Related software:
Cytoscape
Data visualization software on LifeSciSoft]]> Tue, 17 Apr 2012 23:31:27 +0000 http://www.lifescisoft.com/blog/is-big-data-right/
These questions may be easier to answer in life science research than in other fields, but I thought I'd share an article from the Harvard Business Review that might help you in making the decision as well. Basically, Jill Dyche, a VP at DataFlux, suggests asking yourself the following five questions before making any sudden moves:
1) What can't we do today that Big Data could help us do?
2) What skills, technologies, and existing data development practices do we have in place that could help kick-start a Big Data effort?
3) What would a proof-of-concept look like, and what are some reasonable boundaries to ensure its quick deployment?
4) What determines whether we green light Big Data investment?
5) Can we manage the changes brought by Big Data?

Sure, some of these questions are more relevant to life science data than others, but they're all still good to ask.

You can find the full article here: How to Avoid the Big Data "Gotcha's"

Related software information:
Bioinformatics software
Omics software]]> Tue, 17 Apr 2012 21:18:30 +0000 http://www.lifescisoft.com/blog/perkinelmer-releases-ensemble-for-biology-informatics-suite/
Focused on the needs of the pharmaceutical and biopharma industries, Ensemble for Biology has a strong data management focus but also has a multitude of features for collaboration, regulatory compliance and IP. PerkinElmer has positioned it as an end-to-end solution, supporting initial research, downstream development, and ultimate quality control and quality assurance.

They don't call it a LIMS explicitly, but it sure sounds like one. They also say that it's useful for government and academic researchers in addition to pharma and biopharma, but it seems like it does a lot more than those academics would need it to (and I'm going to make the not-so-wild guess that the pricing would reflect that). Let's call Ensemble for Biology what it is: a very fully featured LIMS that's geared heavily towards industry.

More info:
Press release from PerkinElmer
Ensemble for Biology details on LifeSciSoft
LIMS on LifeSciSoft
Information Management & Data Management software on LifeSciSoft ]]> Tue, 17 Apr 2012 00:12:51 +0000 http://www.lifescisoft.com/blog/ruro-freezerpro-basic/
FreezerPro Basic will be somewhat stripped down, having removed features "needed to manage a larger lab". The important aspects of barcode support and excel integration remain intact, however.

FreezerPro Basic will retail for $1599. Academic and government labs will get a $300 discount.

More information:
News release from RURO
Sample management software on LifeSciSoft
]]> Mon, 16 Apr 2012 14:58:03 +0000 http://www.lifescisoft.com/blog/eagle-genomics-symposium-presentations/ http://www.eaglegenomics.com/2012/04/presentations-from-eagle-genomics-second-symposium/

Related software:
Genomics software on LifeSciSoft
Bioinformatics software on LifeSciSoft]]> Fri, 13 Apr 2012 18:20:58 +0000 http://www.lifescisoft.com/blog/cytosure-interpret-software-update/
More information:
Microarray software on LifeSciSoft
Cytogenetics software on LifeSciSoft]]> Thu, 12 Apr 2012 18:36:20 +0000 http://www.lifescisoft.com/blog/clc-bio-simplifies-software-offering/
In what we presume is recognition that many users will require all of the functionality of the more expensive CLC Main Workbench, the price of CLC Main Workbench was pretty dramatically reduced for all users. Industry users will now pay $1999 for a static, single license or $3999 for a network license, and academic users will pay $399 for a static, single license or $799 for academic customers.

More information:
CLC Main Workbench on LifeSciSoft.
Genomics Software on LifeSciSoft

Edit:
We found a bit more info we wanted to share... Users of the discontinued CLC bio software that are still in the maintenance and updates program can update to CLC Main Workbench for FREE. See here for more details: http://clcsoftware.com/how_to_upgrade.php. Also, all academic users can purchase CLC Main Workbench for only $179 until the end of May via a credit card purchase through the CLC bio website.]]> Thu, 12 Apr 2012 13:42:07 +0000 http://www.lifescisoft.com/blog/most-popular-genomics-software/ HighWire to do a few full-text searches to see what the most referenced genomics software is. We had a few criteria:
• The software has to be able to perform sequence analysis on NGS data sets.
• In keeping with site tradition, non-commercial software isn't included.
• Number of references is presumed to be analogous to popularity (yes, that's a flawed assumption but we're doing this for fun so we don't really care).

The short list of software that we came up with was Avadis NGS, CLC Genomics Workbench, GenomeQuest, DNAnexus, Partek Genomics Suite, and Sequencher. Yes, we know this is not a comprehensive list and we thought it up in all of 3 minutes, so if you think we've left something important out go ahead and call us out on it.

The all-time numbers that HighWire returned were:
Sequencher - 4061
Partek Genomics Suite - 320
CLC Genomics Workbench - 102
DNAnexus - 3
GenomeQuest - 3
Avadis NGS - 2

Of course this was a wantonly biased game; Sequencher has been around since 1991, around the time that many current grad students were entering elementary school. To balance the field and remove bias for older software packages, we changed the search to only include from last April (2011) to the present. The results then looked like this:
Sequencher - 374
Partek Genomics Suite - 133
CLC Genomics Workbench - 84
DNAnexus - 2
Avadis NGS - 2
GenomeQuest - 1

Seems like even today, Sequencher is the run-away favorite, with Partek and CLC battling it out for second. The rest of the pack has a lot of catching up to do.

So... What do you think? Do the results meet your expectations? What NGS software do you use in your lab or at your institution?

Related topics:
Genomics software on LifeSciSoft]]> Wed, 11 Apr 2012 23:24:16 +0000 http://www.lifescisoft.com/blog/clc-bio-new-versions/
CLC Genomics Workbench 5.1
• There is a new "broken pair mate locater tool"
• MiSeq multiplexed data is now directly supported
• Ion Torrent paired protocols are now supported for fastq and sff files
• Aligned fasta import and export is now supported

CLC Genomics Server 4.1
• MiSeq multiplexed data is now directly supported
• Ion Torrent paired protocols are now supported for fastq and sff files
• Aligned fasta import and export is now supported

CLC Sequence Viewer 6.6.2
• Aligned fasta import and export is now supported
• A bug that occurred when performing restriction cloning in regions with single-stranded DNA is now fixed

CLC Main Workbench 6.6.2
• Aligned fasta import and export is now supported
• A bug that occurred when performing restriction cloning in regions with single-stranded DNA is now fixed

More information:
CLC Genomics Workbench on LifeSciSoft
CLC Genomics Server on LifeSciSoft
CLC Main Workbench on LifeSciSoft
Genomics software on LifeSciSoft]]> Wed, 11 Apr 2012 16:38:54 +0000 http://www.lifescisoft.com/blog/network-visualization-software/
Describing itself as "like Photoshop but for data," Gephi won't replace your current statistics or graphing software, but rather takes the data and projects it in different (read: "more useful") ways in an attempt to allow the user to get a better feel for the data and thereby facilitate reasoning.

Gephi has a plethora of different ways to visualize data and has multiple layout algorithms which provide varying degrees of efficiency and quality for various visualizations. There is also a large collection of plugins, and plugins are automatically updated from within Gephi. Gephi can handle data sets of up to 50k notes and 500k edges, which is certainly still small enough to frustrate many -omics bioinformaticians, but it is designed to work on a regular, everyday computer so it needs to instill limits somewhere. The benefit to the data set limitation is that data visualizations can be manipulated in real time.

The best and worst parts of Gephi are likely the same as with almost any open-source, free software: it's open-source and free. Open source software, while allowing the development of great functionalities, tends to become bloatware over time, reducing performance while eating up system resources. Free software is unsupported and tends to fall off the map eventually as people stop caring about it. Now neither of these things are certainties, and we hope that we're wrong, but there's a reason that we only list commercially supported software on LifeSciSoft - everything else tends to fall off the map at a rapid clip.

For now, though, Gephi is here and it does some really nifty things with large data sets. If you have a minute, try it out. Heck, it's free so why not?

Links:
Gephi
Data visualization software on LifeSciSoft]]> Mon, 09 Apr 2012 19:58:56 +0000 http://www.lifescisoft.com/blog/1000-genomes-data-aws/
The catch? If you plan on doing anything with it you may need to upgrade your computing capabilities ... by a few powers of 10. The 1000 Genomes Project data currently stands at a whopping 200 terabytes. That's "my closet is exploding with hard drives" kind of data.

Still, if you're the type that's long since fallen head-over-heels in love with genomic data, you can find find cloud access to the 1000 Genomes Project data through AWS here: http://s3.amazonaws.com/1000genomes/

More information:
1000 Genomes website
Genomics Software on LifeSciSoft. ... If you're even thinking about doing anything with all that data, you'll need some.]]> Tue, 03 Apr 2012 20:03:05 +0000 http://www.lifescisoft.com/blog/elements-of-bioinformatics/
It's much more fun to see than read about. You can check it out here: http://www.eaglegenomics.com/2012/04/the-elements-of-bioinformatics/.

Related software:
Bioinformatics software on LifeSciSoft]]> Tue, 03 Apr 2012 13:51:03 +0000 http://www.lifescisoft.com/blog/integromics-realtime-statminer-4.3-tibco-spotfire/
New features in the latest version of RealTime StatMiner include:
• Automated processing
• Improved interactive visualizations
• Global normalization for mRNA studies
• Advanced quality controls
• Integration with the Ingenuity Pathway Analysis (IPA) and the TIBCO Spotfire Webplayer

For more information:
Press release from Integromics
RealTime StatMiner on LifeSciSoft
Genomics Software on LifeSciSoft
Genetics Software on LifeSciSoft]]> Mon, 02 Apr 2012 16:30:17 +0000 http://www.lifescisoft.com/blog/definiens-3rd-symposium/ • Expanding the Frontiers in Translational Medicine
• Improving Disease Understanding and Safety Models in Drug Development
• Quantitative Digital Pathology for Clinical Decision Support
• Towards Diagnostic Biomarkers and Personalized Medicine
• Advanced Image and Data Analysis in Basic Research

Each session consists of a series of talks.

For more information:
3rd International Definiens Symposium program
Imaging Software on LifeSciSoft
More info on software by Definiens on LifeSciSoft]]> Fri, 30 Mar 2012 15:55:13 +0000 http://www.lifescisoft.com/blog/clc-qc-report-genomics-workbench/
More info:
CLC bio plugins
Genomics software on LifeSciSoft]]> Fri, 30 Mar 2012 15:29:24 +0000 http://www.lifescisoft.com/blog/pistoia-alliance-ngs-conference/
Pilot solutions for delivering cloud-hosted NGS data will be highlighted. These pilots, designed by three consortia, were developed in response to an RFP from Pistoia. Other noteworthy event include the presentation of the $15000 prize to the winner of the Sequence Squeeze competition to design an open-source solution to genomic data compression and tn interactive session allowing attendees to comment on proposed new projects.

More information:
Pistoia Alliance Annual Conference website
Genomics software on LifeSciSoft]]> Fri, 30 Mar 2012 15:18:50 +0000 http://www.lifescisoft.com/blog/cloud-biolinux-genomics/
Packaged in Cloud BioLinux are a host of GUI and command-line interfaces and over 135 bioinformatics tools for a plethora of genomics applications including alignment, clustering, assembly, editing, visualization, and phylogeny. For all you curious Linux enthusiasts, the virtual machines are based on Ubuntu.

A bit of credit to the guys at Eagle Genomics for noting that the tools available for Cloud BioLinux and those available for DebianMed will likely one day be interchangeable as they're both Debian-derived. This would be a lovely marriage as the established DebianMed's larger package library with Cloud BioLinux's easy cloud integration.

More information:
Paper in BMC Bioinformatics

]]> Fri, 30 Mar 2012 11:49:24 +0000 http://www.lifescisoft.com/blog/geneious-pro-5.6-beta/
• New parent-descendant tracking. Geneious Pro 5.6 tracks cloning changes such that changes to parent sequences are propagated to all descendants.
• Improved large-scale data handling. The software has been optimized for larger data sets.
• Improved variant calling accuracy. Geneious Pro 5.6 reduces false SNP calls due to sequencing errors by accounting for strand bias.
• New annotation table and menu layout. The annotation table has been integrated in the sequence view.

For more information:
Announcement from Geneious
Genomics Software on LifeSciSoft]]> Wed, 28 Mar 2012 16:27:29 +0000 http://www.lifescisoft.com/blog/sympletic-4th-user-conference/
Registration and conference information can be found here

Related information:
ELN on LifeSciSoft
LIMS on LifeSciSoft]]> Wed, 28 Mar 2012 16:15:55 +0000 http://www.lifescisoft.com/blog/filgen-qlucore-omics-expolrer/ News article on GenomeWeb
More info on Omics Explorer
View all omics software on LifeSciSoft
Genomics software on LifeSciSoft]]> Wed, 28 Mar 2012 16:03:56 +0000 http://www.lifescisoft.com/blog/agilent-releases-genespring-12/
The Pathway Architect module allows researchers to use WikiPathways in order to view and analyze pathway content. Mapping across annotation databases is accomplished through integration with BridgeDB. (Both WikiPathways and BridgeDB are publicly available resources). Data from "single-omic" experiments is merged with others to form "multi-omic" data sets that can be jointly analyzed.

In addition to Pathway Architect, GeneSpring 12.0 includes an NGS module. The NGS module was (unsurprisingly) validated using Agilent's SureSelect target enrichment platform. The new GeneSpring NGS module contains a QC manager, DNA-seq workflows, and RNA-seq workflows.

GeneSpring 12.0 also features new customization capabilities. Jython and R programming language support has been added.

GeneSpring version 12.0 is available free to all existing GeneSpring customers during the evaluation period which runs until August 17th.

For more information:
Press release from Agilent
Read more about GeneSpring on LifeSciSoft
View all omics software on LifeSciSoft
Genomics software on LifeSciSoft]]> Wed, 28 Mar 2012 15:41:01 +0000 http://www.lifescisoft.com/blog/perkinelmer-ensemble-chemistry-informatics/
Ensemble for Chemistry promises to make chemistry labs more efficient by integrating experiment planning, data management, compound and reaction information, and collaboration tools. Ensemble for Chemistry will also be able to pull data from various sources, such as electronic laboratory notebooks (ELNS) and Laboratory Information Management Systems (LIMS). It also integrates the functionality of ChemDraw and ChemOffice.

For more information:
Ensemble for Chemistry
Cheminformatics Software]]> Tue, 27 Mar 2012 14:19:20 +0000 http://www.lifescisoft.com/blog/macvector-file-support/ via Twitter that they plan to add support for annotating sequences from GFF, BED, GFT, and GFF3 files in their next release. They're also seeking people who use these files (presumably for beta testing, although they make no indication of such).

You can get more information on MacVector on LifeSciSoft, or see all software for genomics.]]> Wed, 21 Mar 2012 14:38:51 +0000 http://www.lifescisoft.com/blog/geneious-microsatellite-plugin/
The new plugin allows users to import their data and provides a simple, graphical environment to allow the user to simply and quickly perform allele calls. Features of the new plugin include:
• Import traces in .fsa format and store them in the Geneious database
• Viewing of multiple traces simultaneously
• Call peaks, match ladders and bin automatically
• View genotype results in allele table views
• Export peak calls and genotypes in CSV format for further analysis
• Click and drag to adjust trimmed regions
• Add and remove peaks for total control
• Add, remove and edit bins including click and drag to resize
• Zoom in and customize single or multiple traces

You can download a free trial of the Geneious Microsatellite Plugin on the Geneious website.

Related software:
Genomics Software ]]> Tue, 20 Mar 2012 14:38:52 +0000 http://www.lifescisoft.com/blog/in-silico-biology-imc-5-1/
• Integration of NCBI Blast+
• Additional parameters for primer design
• Improved filtering function of the restriction enzyme list
• A bug fix that corrects reading more than 20,000 reads in 16SrRNA metagenome analysis
• A filtering-out function of the IMC original features and qualifiers from GenBank or EMBL format files
• A drawing and printing function of GC content or GC skew plot graphs

More information on IMC can be found on LifeSciSoft.

Additional Information:
Version update release from IMC
Genomics Software on LifeSciSoft
Genetics Software on LifeSciSoft ]]> Mon, 19 Mar 2012 15:43:18 +0000 http://www.lifescisoft.com/blog/simulations-plus-malaria/ MedChem Studio, MedChem Designer , ADMET Predictor , and GastroPlus software, they designed five novel compounds then demonstrated that four of the five would exhibit some inhibition, and one would show "very potent inhibition at a level suitable to be a therapeutic agent".

Is it time for a digital drug design revolution? Well, maybe. Dr. Robert Clark, director of drug design for Simlulations Plus readily admitted that "[...] inhibiting the parasite does not necessarily mean that this molecule would be a good drug. There are many more properties that must be acceptable and years of development needed before that could happen." Even so, with pharmaceutical drug development growing into an ever-longer process, the prospect of accurate drug design and preliminary testing completely in silico would be a welcome relief.

You can read the press release from Simulations Plus here: press release link]]> Sat, 17 Mar 2012 01:23:03 +0000 http://www.lifescisoft.com/blog/pharsight-pks-meeting/
Registration for both events is extremely limited. For more information or to inquire about attending, visit Pharsight's events page.

Related software information:
Pharmacology software]]> Thu, 15 Mar 2012 23:34:39 +0000 http://www.lifescisoft.com/blog/appistry-mendelspod/
The podcast can be listened to here: http://mendelspod.com/podcast/appistry

Related software information:
Genomics Software
Bioinformatics Software]]> Tue, 13 Mar 2012 19:37:09 +0000 http://www.lifescisoft.com/blog/definiens-digital-pathology-software/ USCAP annual meeting in Vancouver, Definiens software for digital pathology will be highlighted in a series of talks by Definiens users. We're big proponents of seeing software in action, so these talks will be a good opportunity for any pathologists who will be at USCAP to see some results of Definiens software put to use.

The talks that will feature Definiens digital pathology software are:
• [2139] Novel Quantitative Image-Analysis Based Scoring Technique for In-Situ Assessment of mRNA in Archival Tumor Tissues: Strong Correlation between Manual and Automated Schemes
• [1389] Automated Image Analysis and Scoring of Tartrate Resistance Acid Phosphatase Preparations Authors: Bryan Dangott, Mohamed Salama
• [1634] Validation of Automated Image Analysis for Hematopathology
• [1487] Notch/HES1 and PARP1 Protein Co-Expression among B-Lymphoblastic Leukemia/Lymphoma Patients (pts) Predicts Good Prognosis

More information about Definiens software can be found here on LifeSciSoft:
Developer XD
Server XD
Architect XD
Viewer XD
Tissue Studio
LymphExpert
]]> Tue, 13 Mar 2012 19:25:50 +0000 http://www.lifescisoft.com/blog/pittcon-software/
Bruker announced two new software offerings today. One is CMC-assist, for interpretation of NMR spectra. It enables complex analysis of spectra from 1D 1H datasets, and is aimed at improving throughput and efficiency while being simple enough to be user-friendly to NMR novices. Bruker's other new software is CompassCDS 3.0, for multi-instrument GC laboratories. CompassCDS 3.0 is highly customizable, network deploy-able, includes a number of industry-focused plugins for various applications, and is capable of controlling all of the current Bruker GC's.

Waters announced the launch of its NuGenesis 8 software. Aimed at industry labs, NuGenesis is a data management and workflow solution that aims to help integrate analytical data into organizations business IT systems. Among other functionality, NuGenesis 8 combines the functions of a scientific data management system (SDMS) with an electronic laboratory notebook (ELN), a sample management system, and a regulatory compliance system. NuGenesis 8 is designed to obtain data from disparate sources and also feed data into other IT infrastructures, enabling data to be more easily leveraged on an enterprise level.

Related software:
Spectroscopy software"
Data management software]]> Mon, 12 Mar 2012 16:59:32 +0000 http://www.lifescisoft.com/blog/simulations-plus-admet-predictor-ip/
The IP includes a database of 500 metabolism measurements used in predictions of the Cytochrome P450 hydroxylation reaction, as well as 900 compounds used to build the substrate classification models for UGT enzymes. Simulations Plus CEO Walt Woltosz said that the company will now bundle the metabolism and metabolic site capabilities into one package since they no longer have to maintain separate records for royalty purposes.

More information:
Press Release from Simulations Plus
Pharmacology Software on LifeSciSoft]]> Wed, 07 Mar 2012 19:41:57 +0000 http://www.lifescisoft.com/blog/sage-n-research-io-informatics-proteomics/
You can read more on GenomeWeb.]]> Wed, 07 Mar 2012 19:25:34 +0000 http://www.lifescisoft.com/blog/motif-discovery-in-biological-networks/
In the words of the authors: "First, we extend subgraph searching algorithm Enumerate Subgraphs (ESU) to efficiently search non-treelike subgraphs of which the probability of occurrence in random networks is small. Then, we classify isomorphic subgraphs into different groups. Finally, we use hierarchical clustering method to cluster subgraphs, and derive a consensus motif from the clusters. Our algorithm is applied to the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae. The experiment results show that the algorithm can efficiently discover motifs, which are consistent with current biology knowledge. And, it can also detect several consensus motifs with a given size, which may help biologists go further into cellular process."

You can find the abstract and [paid] full-text of the paper here.

More information on bioinformatics software.]]> Tue, 06 Mar 2012 16:07:12 +0000 http://www.lifescisoft.com/blog/dnanexus-to-launch-operating-system-for-genomics/
To find out exactly what that "operating system" will look like, or will do, we'll just have to be patient and wait.

Read the original article on Medgadget
Genomics software on LifeSciSoft]]> Mon, 05 Mar 2012 21:58:25 +0000 http://www.lifescisoft.com/blog/geneious-launches-2012-geneious-challenge/
Plugins can be developed using the Geneious public API, and all plugins will be donated to the Biocode commons to allow for their open use and continued development. All entries must be open-source and Geneious is requiring that they are " released either under the LGPL 2.0+ or similar." The winner will be chosen by popular vote at the iEvoBio meeting.

For more information, see the Geneious Challenge webpage.

Related information:
iEvoBio website
Genetics Software on LifeSciSoft]]> Mon, 05 Mar 2012 17:09:52 +0000 http://www.lifescisoft.com/blog/ensembl-66-released/
• Human genome assembly updated to GRCh37.p6
• Short sequence variants are now updated to dbSNP 135
• There is a new regulatory consequence table
• There is a new "region report" tool that allows exporting of genomic information via a web interface or perl script
• The Coelacanth (Latimeria chalumnae) has been added
• The assembly for Ciona intestinalis is updated

Related stuff...
e66 announcement from Ensembl
Ensembl
Genomics Software]]> Fri, 02 Mar 2012 16:12:11 +0000 http://www.lifescisoft.com/blog/patch-to-avadis-ngs-13/
"* A new analysis step Find Significant Regions to compare generic regions across groups of conditions
* Ability to trim poorly aligned portion of a read at the 3′ end
* Creation of Multi-Sample Reports from the import of MiSeq results
* Improvements to the novel small RNA type detection"

Current Avadis NGS customers can quickly update the new version through the menu.

More information:
Patch update notification from Strand Life Sciences
Avadis NGS on LifeSciSoft]]> Wed, 29 Feb 2012 21:23:38 +0000 http://www.lifescisoft.com/blog/make-music-from-your-genes/
So this new company Portable Genomics, is developing software that will allow people to visualize their personal genomic data on their smartphones (presuming they have genomic data and have access to it, of course). If that isn't cool enough as-is, they have this side project called GeneGroove, which is currently up and running and usable. What it does is allow iPhone users to upload their 23andMe data into GeneGroove via iTunes then PLAY IT AS MUSIC ON THEIR PHONE.

Yes, we think that's SO cool that we put it bold and in all caps, interweb etiquette be damned.

In any case, if you're a 23andMe customer, stop reading this and get to their site already. When you make your gene music, share it with us! We want to hear it!

Links:
GeneGroove
Portable Genomics]]> Wed, 29 Feb 2012 17:27:21 +0000 http://www.lifescisoft.com/blog/rna-seq-atlas/
RNA-Seq Atlas contains data expression profiles not only from RNA-seq experiments, but also from microarrays. It can be used to compare expression profiles between tissues, including between normal and tumor tissues, explore pathway profiles, and explore common or diverse expression profiles between tissues. You can also download the entire RNA-Seq Atlas database in tab delineated format.

Links:
RNA-Seq Atlas
Article about the RNA-Seq Atlas in Bioinformatics (PubMed listing)
Databases on LifeSciSoft
Transcriptomics Software on LifeSciSoft]]> Tue, 28 Feb 2012 21:40:39 +0000 http://www.lifescisoft.com/blog/x-gen-congress-genomics-data-conferences/
Each conference will be broken into different programs. The Genomic Data Analysis and Interpretation conference will have programs on structural variation analysis, analysis of non-coding RNA, NGS data analysis and interpretation, and epigenetics. The Sequencing Data Storage and Management conference will have programs on infrastructure to support sequencing research, data transfer and storage, and speeding up de novo assembly. A plenary keynote session will comprise both the end of the Genomic Data Analysis and Interpretation conference and the beginning of the Sequencing Data Storage and Management conference.

For more information on the conferences, see the X-Gen Congress & Expo website.

Related links:
Genomics Software on LifeSciSoft
All 'Omics Software]]> Mon, 27 Feb 2012 17:26:19 +0000 http://www.lifescisoft.com/blog/noldus-workshop-behavioral-research-software/
Noldus' flagship behavioral research software, The Observer XT, will be the topic of its own workshop where Noldus will be discussing features and functions in the latest version (The Observer XT 10.5). Also on the schedule are a session on conducting tests with Noldus' new Stationary Observation Lab and a session on working with digital video.

More information:
Workshop information from Noldus
Behavioral Research Software on LifeSciSoft]]> Mon, 27 Feb 2012 16:51:38 +0000 http://www.lifescisoft.com/blog/eagle-genomics-commences-second-annual-bioinformatics-survey/
You can take the survey here: http://www.surveymonkey.com/s/F8S7DDW

Additional information:
Announcement from Eagle Genomics
Bioinformatics Software on LifeSciSoft
Genomics Software on LifeSciSoft]]> Fri, 24 Feb 2012 14:29:18 +0000 http://www.lifescisoft.com/blog/amazon-launches-simple-workflow-service/
So what? Well, if you're a bioinformatician your life may be getting significantly easier. Laboratory informatics commonly relies on complex workflows to take data from one system, process it with another system, integrate it with other data, then store it (or something along those lines). Traditionally, tools such as Pipeline Pilot or eHive have provided this functionality, but everything had to be analyzed in-house on standalone machines or by clusters. With Amazon SWF, this is no more.

Sure, previous workflow software had cloud integration to some extent, but such functionality was almost always tacked on as an afterthought, and most often it just didn't work that well. Now, the a workflow solution has been designed specifically with the cloud in mind, allowing you to build workflows that both easily take advantage of cloud computing and storage, but are also easily accessible to any computer with an internet connection, allowing greater and easier trans-organizational coordination which improve consistency and reproducibility across large organizations. All that adds up to greater efficiency in bioinformatics.

One drawback - no Perl support, so if you use Perl you'll need to write a script in a supported language to send calls between your Perl scripts and SWF. If that's the worst thing we can foresee about it, we'll take it.

More info:
Amazon SWF
Bioinformatics software on LifeSciSoft]]> Thu, 23 Feb 2012 15:12:56 +0000 http://www.lifescisoft.com/blog/simulations-plus-to-hold-gastroplus-workshops/
• March 19-21, Boston, Massachusetts - Introductory GastroPlus™ Simulation and Modeling Workshop
• April 23-27, Durango, Colorado - Advanced GastroPlus™ Simulation and Modeling Workshop for Drug Absorption, Pharmacokinetics, and Pharmacodynamics
• May 16-18, Beijing, China - Introductory GastroPlus™ Simulation and Modeling Workshop
• May 21-23, Shanghai, China - Introductory GastroPlus™ Simulation and Modeling Workshop

There is a fee to attend the workshops. For more information, see: http://simulations-plus.com/workshop.aspx?eID=1

Additional Information:
GastroPlus information on LifeSciSoft
All Simulations Plus software on LifeSciSoft
More Pharmacology Software on LifeSciSoft]]> Wed, 22 Feb 2012 20:17:21 +0000 http://www.lifescisoft.com/blog/bioteam-releases-minilims-for-ion-torrent-pgm/
For those not familiar with it, MiniLIMS is a light, out-of-the-box LIMS deployment specifically for the management of data from next-gen sequencers. It already has versions for the Roche 454, Illumina GAIIx, and Illumina HiSeq, and has plans to support PacBio and SOLiD systems later this year (although I personally think they may as well skip SOLiD, as that ship has sailed).

For more information:
BioTeam announcement
More LIMS software ]]> Wed, 22 Feb 2012 18:02:51 +0000 http://www.lifescisoft.com/blog/metaxcms-untargeted-metabolomics-data/
metaXCMS is an evolution of the original XCMS software. Whereas the original allowed direct comparison of two sample groups, metaXCMS "enables meta-analysis of an unlimited number of sample classes to facilitate prioritization of the data and increase the probability of identifying metabolites causally related to the phenotype of interest".

metaXCMS requires the original XCMS (the input to metaXCMS is the XCMS output), and can be run on Windows or Unix operating systems. For Windows, you'll need to have R and GTK+ installed, and for Unix you'll only need R. XCMS and metaXCMS are freely available for download.

More information:
metaXCMS article in Nature Protocols
metaXCMS page on the Scripps website
Metabolomics software on LifeSciSoft
Mass Spec software on LifeSciSoft]]> Tue, 21 Feb 2012 18:22:20 +0000 http://www.lifescisoft.com/blog/med-pc-64-bit-released/
Med-PC customers with an active maintenance agreement can request an upgrade CD at no charge.

More information:
News release
http://www.lifescisoft.com/blog/accelrys-tech-summit-3/
More information:
Accelrys community message
Accelrys Tech Summit 3 Registration
More info on Accelrys software]]> Mon, 20 Feb 2012 13:30:23 +0000 http://www.lifescisoft.com/blog/complete-genomics-software-partners-program/
DNAnexus will be providing an "instant genomics data and analysis center" leveraging its existing cloud-based solutions for human genome sequencing data generated by Complete Genomics. Golden Helix will be providing its SNP and Variation Suite in order to "quickly uncover statistically significant genotype-phenotype associations or causal variants in large-scale data". Ingenuity Systems will be providing its new Ingenuity Variant Analysis™ software, which will help filter and prioritize variants from human re-sequencing studies.

More information:
View the press release
Genomics Software on LifeSciSoft]]> Thu, 16 Feb 2012 22:12:42 +0000 http://www.lifescisoft.com/blog/agilent-genespring-12/
The list of disclosed new features include:
- Next-generation sequencing analysis for SureSelect target enrichment (DNA and RNA)
- Multi-Omic Analysis for Integrated Biology
- Joint network and pathway analysis for Integrated Genomics
- New Pathway Analysis and Visualizations
- Updated biological annotations and content
- New Statistical Algorithms
- Enhanced Visualizations
- Extensibility Improvements

There will also be a new module for GeneSpring: GeneSpring NGS. GeneSpring NGS will contain tools for whole-genome sequencing (WGS) and will be specifically optimized for target enrichment using SureSelect kits.

More information:
Read the newsletter
GeneSpring GX on LifeSciSoft
GeneSpring Workgroup on LifeSciSoft
More 'Omics software on LifeSciSoft]]> Wed, 15 Feb 2012 14:49:15 +0000 http://www.lifescisoft.com/blog/labguru-brings-users-select-nature-protocols/ Labguru, the collaborative research management web application for researchers and academic labs, has teamed up with Nature Publishing Group to bring high-quality protocols direct to Labguru users. This will make it easier for Labguru users to access and use certain protocols, as well as create plans for experiments that use the protocols.

They've seeded Labguru with 20 protocols which are "some of the most fundamental and widely used in the lab," according to chief Nature editor Chris Surridge. We would hope they are. 20 random or obscure protocols wouldn't be doing many people much good!

Looking for more info?
See the news release from Digital Science.
Read more about Labguru on LifeSciSoft.
Until the end of February, enter to WIN a free year of Labguru for your lab!]]> Mon, 13 Feb 2012 16:54:42 +0000 http://www.lifescisoft.com/blog/biochrom-releases-resolution-software-for-spectrophotometer-control/
Unfortunately, albeit not unsurprisingly, the software currently only works with Biochrom's own Libra spectrophotomoeters, so if you don't have a Libra or don't plan on getting one, you'll probably never get to put Resolution to use. Luckily, there's a bunch of other good software out there to do the job.

More info on Resolution: http://www.biochrom.co.uk/product/58/resolution-advanced-spectrophotometer-software.html

For more spectrophotometry software: http://www.lifescisoft.com/spectroscopy.html?cat=134]]> Fri, 10 Feb 2012 19:19:42 +0000 http://www.lifescisoft.com/blog/more-science-gaming-fun/ Foldit? Well now you have another scientific gaming option. You can now help researchers at MIT, Harvard, and the Max Planck Institute for Medical Research decipher the connectome (the entirety of neural wiring) of the retina!

Researchers at Harvard and the Max Planck Institute have been taking electron microscopy images of ultra-thin sections of the mouse retina in order to establish the location of all of the neural processes. To help map those processes, Sebastian Seung MIT devised a computerized system which was first displayed back in 2009, but to do so with sufficient accurately it still needs human guidance. And how do we recruit large-scale human contribution? GAMES!

Seung subsequently developed Eyewire to recruit the masses to help guide the computer through the neural connections. A person playing the game can pick a neuron, and the AI system will start coloring along that neuron until it gets confused, at which point it asks for guidance. The player than chooses the correct path, and the process is repeated until the neuron is fully colored in. By providing the system with input, the player is also training the AI, such that it will need less human input with time.

Another interesting challenge is the amount of data this requires. A human brain is about a 1130 cubic centimeter object. The slice of mouse retina that Eyewire is currently dealing with is 300 x 350 x 80 micrometers, or 8.4*10^-6 cubic centimeters ... but it takes a full terabyte of storage space. Do the math and you'll find that a connectome for an average human brain would then require over 134 exabytes of storage space (1 exabyte = 1,000,000 terabytes). Obviously, that presents a bit of an IT challenge.

But those worries are for another day. For now, let's have some fun and draw some neurons!

More info: http://www.mit.edu/newsoffice/2012/connectome-0207.html
The game: http://eyewire.org/]]> Fri, 10 Feb 2012 15:17:13 +0000 http://www.lifescisoft.com/blog/pistoia-alliance-eagle-genomics-cycle-computing-pharma-rnd/
The to-be-developed platform, dubbed the Sequencing Analysis Platform, is slated for commercial release around the middle of 2012. The proof of concept is due much earlier, and is scheduled to be demonstrated in March at the annual Pistoia Alliance Conference in Boston.

The award by Pistoia also grants Eagle Genomics and Cycle Computing a joint $50,000 prize.

For more information: Bioinformatics Software on LifeSciSoft
Genomics Software on LifeSciSoft ]]> Thu, 09 Feb 2012 16:57:56 +0000 http://www.lifescisoft.com/blog/accelerated-technology-laboratories-sample-master-lims-boot-camp/
For more information on the Sample Master LIMS Boot Camp: http://www.atlab.com/index.php?option=com_jcalpro&Itemid=83&extmode=view&extid=10
For more information on Sample Master LIMS: http://www.lifescisoft.com/sample-master.html]]> Wed, 08 Feb 2012 18:39:33 +0000 http://www.lifescisoft.com/blog/integromics-to-develop-low-cost-methods-for-clinical-genomics/
While it's inevitable that the costs involved in clinical NGS data analysis and management will drop, the big question is how fast. There is obviously an existing and rapidly growing need for faster and lower-cost methods, and we'll see how much this collaboration can accomplish when they release their initial results in the 4th quarter of 2012.

More information: http://www.integromics.com/genomics-and-proteomics-data-management/integromics-partners-with-fpgmx-to-develop-low-cost-methods-for-clinical-genomics

More information on Integromics software solutions: http://www.lifescisoft.com/catalogsearch/result/?q=integromics]]> Wed, 08 Feb 2012 14:36:36 +0000 http://www.lifescisoft.com/blog/labguru-hosts-webinar-series/ series of webinars providing an introductory tour to their highly-acclaimed scientific data management software.

While all the webinars currently scheduled (eight through March 1st) are all introductory, they'll be hosting topic-specific ones in the future as well which will show more specific capabilities.

For more information on the webinars or to register go to: http://www.labguru.com/webinars

You can find more information on Labguru right here on LifeSciSoft: http://www.lifescisoft.com/labguru.html

...and if you didn't hear, in February you can WIN a year of Labguru for your lab! More details here: http://www.lifescisoft.com/contest]]> Tue, 07 Feb 2012 19:30:46 +0000 http://www.lifescisoft.com/blog/simulations-plus-on-faculty-for-odd12/
Enrollment in the workshop is limited to 40 attendees. For more information, visit: http://www.ddfint.org/odd12/index.htm

For can find more information on Simulations Plus software on LifeSciSoft:
GastroPlus™
ADMET Predictor™
MedChem Designer™
DDDPlus™
Medchem Studio]]> Mon, 06 Feb 2012 20:40:34 +0000 http://www.lifescisoft.com/blog/strand-life-sciences-avadis-ngs-13/ http://blog.avadis-ngs.com/2012/02/release-announcement-version-1-3/

You can also find more information on Avadis NGS right here on LifeSciSoft: http://www.lifescisoft.com/avadis-ngs.html

Related Information:
Genomics Software on LifeSciSoft]]> Wed, 01 Feb 2012 17:04:16 +0000 http://www.lifescisoft.com/blog/pistoia-alliance-squeeze-competition/
Presently that opportunity comes in the form of a $15,000 prize offered up by The Pistoia Alliance. They're sponsoring a competition - the Sequence Squeeze Competition - that hinges around who can take a set of NGS data (sequence reads and quality scores) and compress it as much as possible while retaining 100% of the information.

There is a four-person judging panel and the winner will be determined based on compression ratio, compression time, compression memory, decompression time, decompression memory, header mismatches, sequence mismatches, and quality score mismatches. If you're interesting in entering, you can find out how here: http://www.sequencesqueeze.org/how-to-enter/index.html

Related Information:
Genomics Software on LifeSciSoft
Bioinformatics Software on LifeSciSoft]]> Wed, 01 Feb 2012 16:38:40 +0000 http://www.lifescisoft.com/blog/free-year-of-labguru/ http://www.lifescisoft.com/contest]]> Wed, 01 Feb 2012 14:40:18 +0000 http://www.lifescisoft.com/blog/expasy-down-for-maintenance/
Related info:
Bioinformatics Software on LifeSciSoft]]> Fri, 27 Jan 2012 18:14:20 +0000 http://www.lifescisoft.com/blog/wheres-your-eln/ Nature News editorial highlights the ever-increasing use of ELNs - electronic laboratory notebooks - and other laboratory and data management software. With more and more labs going fully digital, they discuss the auspicious lack of paper in many modern laboratories, and the efficiencies created by converting.

The writer of the editorial, Jim Giles, also makes a bold prediction. While previous iterations of ELNs, LIMS, and SDMS didn't combine the ease of use and broad functionality to make them a viable replacement for the paper notebook in many labs, he predicts that the current generation of offerings does exactly that and alludes to the end of the centuries-long reign of the paper laboratory notebook.

More information on Electronic Laboratory Notebooks]]> Fri, 27 Jan 2012 14:46:33 +0000 http://www.lifescisoft.com/blog/have-fun-fold-proteins/ video game about protein folding. No, you're not hallucinating. Yes, we're completely serious.

Foldit is a video game that's crowdsoucing the power of gamers to solve problems in protein structure research. The game uses real protein folding models and asks users to come up with solutions to protein folding "puzzles". The [awesome] catch is that researchers at the University of Washington and the Fred Hutchinson Cancer Research Center are using the solutions that gamers come up with and applying them to actual proteins in order to predict structures and design protein therapeutics. You can now help research cancer, Alzheimer's disease, and AIDS while you play a video game.

Ultimately, Foldit also hopes to collect information on the way humans solve the protein structure puzzles and determine if humans are more efficient than computers. If so, they aim to further use that data to try to teach computers to solve protein folding problems the way that humans do.

If you're thinking that there's no way that this could possibly work, then I hate to break it to you but it already has. Check out this article in Nature Biotechnology: Increased Diels-Alderase activity through backbone remodeling guided by Foldit players]]> Thu, 26 Jan 2012 15:47:40 +0000 http://www.lifescisoft.com/blog/labguru-ipad-app/
And yes, the iPad app is usable with Labguru's free personal subscriptions.

You can get the Labguru iPad app here: DL the Labguru iPad app
You can view the news release on the Labguru blog here: Labguru iPad app news release
And you can learn more about Labguru on LifeSciSoft here: Labguru on LifeSciSoft]]> Wed, 25 Jan 2012 20:43:48 +0000 http://www.lifescisoft.com/blog/labvantage-lims-6/
Some of the improvements are integrated into the new Labvantage from SQL*LIMS, which Labvantage bought from Life Technologies in 2009. For more information you can view the news release from Labvantage or read more about Labvantage's capabilities on LifeSciSoft.]]> Wed, 25 Jan 2012 20:29:01 +0000 http://www.lifescisoft.com/blog/perkinelmer-informatics-lab-services/
Ryan's a great journalist and I don't want to steal his thunder, so I'll let you read the rest of the article here: http://www.fiercebiotechit.com/story/perkinelmer-ceo-arranges-marriage-between-informatics-lab-service-biz/2012-01-13]]> Thu, 19 Jan 2012 17:27:42 +0000 http://www.lifescisoft.com/blog/ab-sciex-indigo-biosystems-mass-spec-software/ announced a collaboration in which Indigo would provide its ASCENT™ software to AB SCIEX for inclusion with its mass spectrometry platforms. The new platforms will target clinical markets, including forensics, clinical research, and clinical trials. Additionally, Indigo BioSystems will be adding some additional "new-generation" algorithms to its ASCENT platform. By teaming up its mass specs with Indigo's software, AB SCIEX hops to "simplify the use of mass spectrometry for those who are accustomed to using easy-to-use lab analyzers."

Even the life science equipment manufacturers are recognizing the importance of providing good software!

Related Information:
Mass Spec Software on LifeSciSoft]]> Wed, 18 Jan 2012 17:03:51 +0000 http://www.lifescisoft.com/blog/ion-torrent-genomics-data-analysis/
Now you may be thinking: if it's going to be open-source, then what's the benefit for Ion Torrent? Well, the software will be specifically designed to analyze the type of whole-genome sequence data produced by Ion Torrent's unique sequencing technology. If a hospital wants that genomic "doctor-in-a-box", they'll have to pick up an Ion Proton Sequencer ... maybe. Anything years into the future is all speculation, and the doctor-in-a-box software isn't going to be around anytime soon.
But the future sure looks cool, doesn't it?

Related information:
Genomics Software]]> Thu, 12 Jan 2012 20:24:25 +0000 http://www.lifescisoft.com/blog/big-data-in-small-places/
There's a new article published in Nature Biotechnology written by two researchers at the Sainsbury Laboratory in the UK, chronicling how this 80-person institution met the challenge of dealing with large amounts of data from high-throughput experiments. One of their answers? Teach everyone bioinformatics just as you would any other discipline of biology necessary to their research and treat bioinformatics as an assay.

In any case, it's a great article and you can read the whole thing here: http://www.nature.com/nbt/journal/v30/n1/full/nbt.2079.html

Other Relevant Information:
Bioinformatics Software on LifeSciSoft]]> Wed, 11 Jan 2012 19:53:09 +0000 http://www.lifescisoft.com/blog/eln-webinar-lab-manager/
"Our panel of experts will talk about the next-generation of ELNs and their dynamic features, serving various applications in the organization. They will also outline a successful implementation strategy, addressing issues such as the relationship between the ELN and other laboratory information systems, the functionalities needed to support different scientific disciplines and the organizational needs related to knowledge management and financial investment."

Agilent, Accelrys, and Waters will be presenting. We think it's a little unfortunate that some of the many smaller ELN developers aren't being given a chance to present, but such is business, I suppose.

If you're interested, you can sign up here: https://www1.gotomeeting.com/register/256825224

More information:
ELN Software on LifeSciSoft]]> Tue, 10 Jan 2012 18:47:40 +0000 http://www.lifescisoft.com/blog/clc-bio-sciengines-supercharge-blast/ teamed up to give BLAST one heck of a turbo boost. Integrating CLC bio's sequence analysis software with SciEngines' FPGA-based RIVYERA S3-5000 platform for massively parallel computing, their preliminary tests have shown a 188x increase speed compared to a Xeon E5520 core. The benchmark test used protein-protein BLAST (BLASTp), but they expect similar results with nucleotide-nucleotide BLAST (BLASTn).

CLC bio's CEO, Thomas Knudsen, had this to say about it: "Several of our big customers estimate that more than 80% of their computing resources are spent on doing BLAST searches and implementing this setup will dramatically increase the overall capacity of their data analysis pipelines. We think this is a very intriguing solution for the enterprise segment of our customers within the biotech, pharma, biofuel, and especially the agro sectors."

While the BLAST software for the RIVYERA hardware platform is still in development, you can catch an early glimpse of it at PAG XX (the International Plant & Animal Genome conference) from January 14-18 in San Diego, California.

Additional Resources:
Genomics Software on LifeSciSoft
Bioinformatics Software on LifeSciSoft]]> Tue, 10 Jan 2012 16:25:12 +0000 http://www.lifescisoft.com/blog/eagle-genomics-genome-content-management/
The one-day symposium currently has 9 speakers lined up including the keynote speaker Tim Hubbard, Head of Informatics at the Wellcome Trust/Sanger Institute. If you *heart* genomics data, this looks to be a great event for you to attend. For more information, visit: http://www.eaglegenomics.com/2011/10/the-next-10-years-of-genome-content-management/
Related Information:
Genomics Software
]]> Mon, 09 Jan 2012 14:24:17 +0000 http://www.lifescisoft.com/blog/biological-data-mapping/ Biomap.org is the brand new blog of Amandeep Sidhu, Ph.D., an experienced bioinformatician, research fellow and systems engineer at Curtin University in Australia, where he is leading the development of a bioinformatics facility. His blog is all about effective data management. So far (it's only been up since December 21st) it's focused on cloud storage and cloud computing, but we're sure as time goes by he'll branch out to other interesting biological data management topics as well.

Perhaps we'll try to recruit him for an interview.]]> Thu, 05 Jan 2012 18:06:35 +0000 http://www.lifescisoft.com/blog/ibm-green-hat/ announced the acquisition of Green Hat, a cloud computing development platform. Green Hat has been around since 1996, but a large acquirer such as IBM will probably boost its visibility and make its use more common.

So what? Well, as GenomeWeb's Matthew Dublin keenly noted: "Getting popular bioinformatics software applications — typically run on clusters or workstations — to operate smoothly on the cloud is still anything but trivial, so a testing environment that allows for some growing pains could prevent lots of frustration and wasted grant money."

Sounds like a solid plus for bioinformatics cloud development.]]> Thu, 05 Jan 2012 16:02:39 +0000 http://www.lifescisoft.com/blog/lims-qna/ LIMS:

Carlton Hoyt: Thanks a bunch for agreeing to an interview, Gloria.

Gloria Metrick: Thanks for asking me.

CH: Correct me if I'm wrong, but I presume a LIMS implementations isn't right for every lab. What is a good indication that a lab or organization could benefit from implementing a LIMS, or even that they're past-due for a LIMS implementation?

GM: Today's questions usually revolve around whether a lab needs a LIMS (Laboratory Information Management System) or an ELN (Electronic Laboratory Notebook). This is a tricky question because both products have been merging and we've seen more new names and acronyms being created to describe them, each year. This is state of our industry, right now, which is a total state of flux. It has been this way for a few years, and will remain so for some years to come, I predict.

The idea of buying either system has to do with how difficult it is to access and manage your data. If you can't create reports, manage the data you're acquiring or come up with the data analysis you need in a timely manner, you should consider finding a laboratory informatics system.

Traditionally, LIMS is sample- and test-based, an ELN is experiment-based. However, because these two continue to merge, you'll find LIMS with ELN-like features and ELNs with LIMS-like features. You'll find that some LIMS are specific to a particular process or industry or ELNs that are focused on specific types of labs. Some software vendors label their products not based on any traditional definition of products but on the industry they're targeting and what label they think will sell the best to that industry. Choose incorrectly, and you could cost your lab quite a lot of money.

The money your lab will lose won't just be the cost of the licenses, but usually some significant amount of services costs, as well, to review your situation, do workflow analysis, business analysis, implementation services, and other services. You can imagine this comes to quite a lot of money fairly quickly.

The best advice I can give to those of you who don't think you want to spend the money on a consultant to assist you is that you need to spend quite a lot of up-front time evaluating your needs. Yes, I mean you need to do a full needs analysis with a requirements document. Then, turn that requirements document in an RFP/RFQ (Request for Proposal/Request for Quote). This sounds like a lot of work. It IS a lot of work. But your choice is that you do it, you bring in a consultant to work with you on it, or you end up throwing away quite a lot of money.

Another factor is that, if your laboratory has anything that is high-volume, you probably do need something akin to a LIMS. For example, analytical labs typically have a high-volume of instrument data that must be managed. This is well-suited to management by a LIMS, for one example.

CH: Besides budget, what are the most important factors to consider when shopping for LIMS?

GM: Look for something that meets your requirements. Ignore the labels. Ignore that you want a LIMS or an ELN or an SDMS (Scientific Data Management System). Your needs aren't based on a label. Your needs are based on the actual work you're doing and the tasks you want to integrate into a piece of software. Your needs should not be based on an older piece of software or a paper system. No system maps well to another system. A new software system will map poorly to a paper system but it won't even map well to a previous piece of software. Every software brand is different, even for items that seem fairly well defined, such as drug stability, instrument management or environmental monitoring.

Another tip: everything looks good in a demo, especially when you're at a conference. In real-life, nothing works quite that well. All those drag-and-drop features need serious programming to finish them off, and anything labeled "out of the box" is suspect.

CH: What's the most common afterthought in a LIMS implementation - what do organizations wish they thought of beforehand?

GM: Reports, data analysis and validation. These are pieces that companies think will be simple or, in the case of validation, straightforward. Often, implementing these "simple" pieces will hold-up the project. If reporting or data analysis are pushed-off to post-deployment, customers find that they didn't build enough into the system to have a good structure for pulling data out and making any use of it. I know of implementations that cost millions of dollars that can't produce decent sets of numbers for analysis without spending huge amounts of manual time to "fix" it all.

I've seen plenty of projects derailed by these items that seem rather trivial compared to the rest of the project. After all, most reporting tools are just drag-and-drop, these days -- how hard could that be, everyone thinks. But, while they might have drag-and-drop interfaces, it belies all the programming and formatting it takes to get it to all work and not even to look particularly attractive, which is important at some companies, especially those sending reports to their customers.

CH: LIMS can be very complex, but there are also "lite" LIMS that are a more out-of-the-box. If a lab wants to implement a smaller-scale LIMS to help them manage their research, are there many good options that can achieve significant productivity gains, and ROI, on a small scale? Alternatively, would you consider there to be a point at which a lab or organization is "too small" for LIMS?

GM: The one-person lab is typically too small for any LIMS. There's just not a high-enough volume of data. And since you're not really sharing your system (usually a spreadsheet) with others, something simple is probably sufficient.

If you have 200 users, you need a commercial system. If they're all in the same lab, buy one software product that matches their needs. But if they're doing a variety of tasks, it becomes more difficult. Still, with 200 users, you need to have a managed platform, share data, use a commercial database with proper record locking mechanisms and this type of thing. So, you need a commercial system. At 200 users, if they're all doing the same thing and something fairly straightforward, you can possibly even buy boxed software, as long as it's scalable to a large number of users.

But the word "scalable" is tricky. Everyone claims their software is scalable but when you hit it with 200 users of something heavy-duty, like a lot of analytical testing, that's a true test of whether it can take the load. Performance testing helps you determine if you bought a system that handles the load, but it's often too late at the point you'll do it to return the software.

If you want to buy a system that will handle a load or has any special qualifications and you don't want to take the easy route of buying the most expensive software on the market, you'd have to do a lot of legwork to meet people at conferences and expositions to ask them what software they're using, what kind of load they're putting onto it, and questions of that sort. Those are the people that can help you. Or, you can hire people like myself to help you navigate the territory.

CH: Don't feel obligated to answer - but do you have any LIMS that you would like to recommend to our viewers? Any personal favorites that stand out to you?

GM: No. I don't have a favorite. As it happens, I'm an expert in the LabWare LIMS and do a lot of implementations with that product. But the issue isn't that I recommend this system as "best" but that that is where I've had an opportunity to build expertise. I get this type of work based on the many years of experience I have with it. I can say for certain that no software, not even this brand that I make so much money with, can service every lab.

For example, I sometimes run into labs that buy software in this highest price category in our industry but can't afford it. Those of us in the industry like to use this car analogy: When you're looking for a car in one price range, you might be tempted by a car that is somewhat higher than your price range. You have to wonder if maybe you could afford to spend just a little bit more because you like the more expensive car so much better than the ones in your price range. If you stretch yourself to buy it, you might find you can't afford to drive it because even the insurance is more expensive, and that wasn't something you thought of. It's the same with software products. I do run into customers that stretch their budget to buy something that is out of their price range, only to find out that the cost of maintenance is higher, training is costlier, everything costs more, and they can't afford all the things it really takes to get the system live because they've overextended themselves. Thus, they've spent a lot of money on something that can never work well for their labs, nor achieve any real goals that they've put forth for it.

---

Gloria Metrick has been working with scientific applications, laboratory informatics and, more specifically, LIMS, for about 25 years. She founded GeoMetrick Enterprises over 15 years ago to provide expertise to labs that need services anywhere from requirements gathering to LabWare LIMSBasic programming, to some general consulting to get them focused in the right direction. She has worked with regulated and non-regulated labs in a variety of industries including (but not limited to) food and beverage, chemical and oil, and pharma / biologicals. GeoMetrick produces a free newsletter and a blog, both titled "Out on a LIMS©: The Blog/Newsletter For People Who Risk Life and LIMS™ On a Daily Basis". Both are focused on issues of our laboratory informatics industry. You can subscribe to the newsletter at http://www.geometrick.com/newsltr_signup.htm, and the Out on a LIMS© blog can be found at http://outonalims.wordpress.com/. For more info on GeoMetrick Enterprises visit http://www.geometrick.com/ or you can reach Gloria directly at Gloria@GeoMetrick.com]]> Wed, 04 Jan 2012 15:45:41 +0000 http://www.lifescisoft.com/blog/accelrys-buys-velquest/ announced today that it is buying software developer VelQuest for $35 million in cash. Accelrys's software offerings previously focused on research & development software, but this purchase extends them into the QA/QC arena.

Accelrys President and CEO Max Carnecchia said: "With the acquisition of VelQuest, Accelrys continues to execute on its strategy of providing a broad, flexible solution set for customers that depend on scientific innovation to bring new products from lab to market more quickly and efficiently. VelQuest's strong products and proven domain expertise in compliance-intensive laboratory operations expand our ability to meet our life sciences customers' critical needs in late stage development, quality control and production."

Indeed, Accelrys' acquisition of VelQuest does take them one step closer to offering a complete end-to-end solution. It should also be an easy integration, as some of VelQuest's software has previously been bundled with Accelrys' solutions.]]> Tue, 03 Jan 2012 16:27:40 +0000 http://www.lifescisoft.com/blog/new-online-software-tool-for-protein-sequence-comparisons-hhblits/ published in Nature, HHblits is 50-100% more sensitive than PSI-BLAST and generates more accurate alignments.

The HHblits tool is available online for public use at http://toolkit.tuebingen.mpg.de/hhblits ]]> Tue, 03 Jan 2012 15:31:47 +0000 http://www.lifescisoft.com/blog/lab-equipment-survey-2011/ published it's end-of-year survey and while a lot of the results are similar year-over-year, there were some very interesting findings that are very telling about the future of the laboratory software industry.

Perhaps most interesting were the results of how scientists expected their use of time will change over the next five years. More than any other response, researchers overwhelmingly thought they would be spending more time in front of a computer. 61% of respondents indicated that they expect their time spent at a computer will increase and only 2% thought it would decrease. That's a huge spread.

Laboratory Equipment also asked their readers what technologies will have a great effect on research labs over the next 5 years. Largely consistent with their reader demographics, analytical instrumentation and mass spectrometry were ranked #1 and #2, respectively, but #3 was a surprise. Only 3 percentage points behind mass spec, 22% of respondents indicated that data search technologies will be important, highlighting the challenging informatics problems that more and more labs face.

It wasn't all positive - only 6% of respondents indicated computational challenges as one of their greatest challenges - but all in all I thought the survey highlighted the important and increasing role that software will play in laboratories moving forward. This is a great opportunity for life science software companies and there will likely be a lot of opportunity for both new applications and growth of existing applications.]]> Tue, 27 Dec 2011 16:52:27 +0000 http://www.lifescisoft.com/blog/cloud-just-the-way-we-do-things/ article in Forbes recently stated that 2011 should go down in history as "the year of the cloud" and that in 2012 cloud will "just be the way we do things". I'm not so sure that in the average life science laboratory things are quite there yet, and they certainly aren't in the average American household, but for those that are a bit ahead of the technology curve, it's clear that things are rapidly moving in that direction. Let's take a quick look at how the industry has moved into the cloud...

LIMS (laboratory information management systems) was probably one of the first sectors in the life science software world to go heavily cloud-based. These days it's almost difficult to find a LIMS that isn't at least partially in the cloud. LabLynx, LabWare, BioData, and most companies that provide LIMS solutions leverage (or at least offer) cloud-based access and storage.

ELNs (electronic laboratory notebooks) are quickly following suit. There's a host of cloud-enabled or cloud-based ELNs, including iLabber Cloud, Scilligence ELN, Symyx Notebook, and LABTrack. While a very small fraction of all ELNs used in life science laboratory are cloud-based, the number is rapidly increasing.

Genomics (and other -omics) has also made a strong and rapid push into the cloud, largely by necessity. The volume of data generated from -omics experiments is too massive for many end-user systems to handle, and many labs simply do not have the capability to effectively manage or analyze their own genomic and transcriptomic data. This is especially true as cost reduction in the sequencer market has made sequencing more accessible to smaller labs. Solutions, such as Illumina's BaseSpace and DNAnexus, have popped up to satisfy the increasing need for data analysis and management. Most service-based sequencing companies have also embraced the cloud as a client-friendly data management solution.

The cloud is far from universally embraced in life science laboratories. There are still many software packages and some entire areas of life science research computing that have yet to take their first steps into the cloud. In time, however, the increasing need to improve accessibility, provide easier data management, and leverage more computing power for data analysis will almost certainly continue to drive life science research applications into the cloud.]]> Thu, 22 Dec 2011 00:31:36 +0000 http://www.lifescisoft.com/blog/agilebio-labcollector-21/
• Improvement of the user interface: LabCollector ELN is now even easier to use
• Multilanguage interface
• Multiple images and files uploads at once
• Task time reporting
• Create and apply workflows for experiments
• Archive function and experiment transfer
• Diagram designer tool: design both simple and complex chemical reactions or experimental diagrams
• Integrated spreadsheet templates compatible with excel
• Merge/compile two or more pages in print / pdf views (report arrangement)
• PDF creation with a tree view summary, images and excel files integration

LabCollector is listed on LifeSciSoft. You can find it here: http://www.lifescisoft.com/labcollector.html
]]> Tue, 20 Dec 2011 16:28:15 +0000 http://www.lifescisoft.com/blog/gene-logic-bankruptcy/ filed for chapter 11 bankruptcy. While they were better known for their services, which included gene expression, genotyping, and bioinformatics, they also developed and sold software for toxicogenomics and gene expression. Their software offering includes the ToxExpress® Program, the BioExpress® System, the ASCENTA® System, and the Genesis Enterprise System® Software.

Ocmium Biosolutions is seeking bidders for Gene Logic, but they're on a tight deadline - the bids are due by January 4, 2012, and the auction is two days later. Regardless, it doesn't look like they'll be making up that $10 million that they purchased it for. Ouch.

Hopefully someone does pick up Gene Logic's assets to continue to develop software for genomics and toxicology applications.]]> Fri, 16 Dec 2011 19:00:00 +0000 http://www.lifescisoft.com/blog/biodata-launches-labguru/
TEL AVIV, December 5, 2011 – BioData Ltd., a scientific software company funded by Digital Science, a division of Macmillan Publishers, today launched Labguru, a research management tool designed for academic labs. Labguru’s customizable and affordable web application helps researchers plan experiments, track progress, share results and comments, manage inventories, and organize related documents, protocols and data. More information is available at www.labguru.com or BioData’s booth 1101 at the American Society for Cell Biology Annual Meeting in Denver this week.

“Labguru helps researchers, principal investigators and lab managers see the big picture of their research without losing sight of the details vital to scientific discovery,” says Jonathan Gross, Founder and Co-CEO of BioData. Labguru is an intuitive web-based interface and email alerts service that helps improve the way researchers:

• Plan experiments
• Track research progress on current projects and long-term goals
• Annotate key results, figures, protocols, and papers
• Build research context by linking papers with protocols, notes, specimens and other key data to facilitate planning, paper and thesis writing
• Find the location of specific reagents and samples anywhere in the lab
• Prevent inventory shortages, duplicate orders, and missed expiration dates
• Schedule use of shared equipment
• Retain knowledge as lab members leave

Labguru is free for individual use. Individuals and labs can access additional sophisticated collaboration, order management, and equipment scheduling features for a nominal monthly fee.

Dr. Eli Lewis, Principal Investigator and Senior Lecturer in the Department of Clinical Biochemistry at Ben-Gurion University of the Negev, praises Labguru for fostering scientific thinking. “I found a paper that discussed a cell type one student was working on and a chemical another was studying and then linked those two students to the paper. One of the students linked it to another student and, in a few hours, a comment thread grew in Labguru as if we were having a mini-conference.”

“I enter projects and milestones that form my long-term vision for the lab,” says Anat Ben-Zvi, PhD, Principal Investigator in the Department of Life Sciences at the National Institute of Biotechnology in the Negev at Ben-Gurion University of the Negev. “All lab members can now understand each experiment in context. We can also connect papers to projects and highlight where we sourced some reagent, gene or idea. For each strain we use, Labguru connects all the needed information for experiments, storage, and ordering from either public databases or data that we previously entered. That saves us quite a bit of time.”

“Many Labguru users say their workdays are again the way they should be: fun. Instead of slogging through dull daily management tasks, they spend more time on research and collaboration,” says Gross. Labguru improves upon the most useful features and workflows in both LabLife, software for laboratory organization that BioData recently acquired, and BioKM, BioData’s prior tool for research collaboration. Researchers currently using these tools can continue to do so through 2013 and receive personal assistance when they migrate to Labguru. About BioData, Ltd.

Based in Boston and Tel Aviv, BioData Ltd. creates digital tools for increasing the productivity of academic and industry laboratories. BioData’s web-based software is currently used by thousands of researchers in hundreds of labs worldwide. Key funding for BioData comes from Digital Science, a division of Macmillan Publishers and sister company to Nature Publishing Group. For more information, visit www.labguru.com.

About Digital Science
Digital Science is a division of Macmillan Publishers Ltd., launched in December 2010 to provide technology solutions for researchers. From intelligent knowledge discovery tools to software applications for the laboratory and decision-support systems for managers, Digital Science combines world-class technology with a resolute focus on scientists and those who support the research process. For more information, visit www.digital-science.com. ]]> Mon, 05 Dec 2011 16:00:00 +0000 http://www.lifescisoft.com/blog/presenting-lifescisoft/ http://www.lifescisoft.com), the largest and most comprehensive source of information on software used in life science research. LifeSciSoft has compiled information on well over 600 different software packages, and aims to be a truly comprehensive directory of life science software information.

“Awareness of life science software is low among life scientists.” explained Carlton Hoyt, Ph.D., Acting CEO of LifeSciSoft. “A lot of the traditional marketing and distribution channels used for physical products are not used for software, and this leaves a big gap in awareness. Because of this, the tables are tilted extra heavily to established companies, who may or may not make the best software. What we aim to do is provide a place where scientists can find information on all the software that is available for use in their field of research so they can choose the one that will help them perform their research most effectively and efficiently.” Co-founder and VP of Development Anthony Latona added “We also wanted to create a platform that both allowed and readily encouraged users to share their experiences and leave reviews – something that is notoriously underutilized in the life sciences.”

LifeSciSoft allows software developers to list their products at no charge, including demonstration videos and screenshots. Software companies wishing to do so can visit http://www.lifescisoft.com/list-your-software for more information.

LifeSciSoft
315 Fair Street
Kignston, NY, 12401
E-mail: info@lifescisoft.com
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