24/02/12: Agilent Launch e-Array Version 7.8
February 24, 2012 by Peter · Leave a Comment
Agilent has announced that e-Array v.7.8 has gone live from 23 February 2012. There are several new features and improvements, which are summarized below. They sound like very nice improvements:
New Features
A New eArray Workspace – Mutagenesis!
The eArray Mutagenesis workspace enables custom design for the Agilent QuikChange Oligo Library Mutagenesis System, a novel method for generating a rationally designed library of mutants. This new system enables researchers to precisely target and mutate every codon in up to 20 regions of 50 amino acids or less. It is an easy and rapid method for mid-throughput mutagenesis that allows customers to complete single amino acid scanning, codon saturation, or combinatorial mutagenesis in a single day. Please note that the QuikChange Oligo Library Mutagenesis System is currently available only through an early customer access program.
Three New Catalog SureSelect Kits – Human All Exon v4, Human All Exon v4 plus UTRs, and Human Methyl-Seq
These new SureSelect Target Enrichment kits are now available in eArray, along with a new SureSelect part number schema.
A New Zebrafish Genome version (Zv9) for Custom SureSelect Libraries!
eArray 7.8 now offers the Zebrafish (Danio rerio) Genome version Zv9 for custom SureSelect Target Enrichment, enabling customers to design their libraries using the most current Zebrafish content.
Additional Enhancements
The eArray Development Team has implemented multiple performance and feature enhancements to improve customer experience.
Performance Optimizations for:
- Faster Bait and Probe Uploads
- Faster Creation of Bait Groups and Probe Groups
- Faster Probe Group Downloads
- Faster Design File Generation – Less waiting for new annotation files during “File Write in Progress.”
Longer Maintenance of Bait Tiling Parameters and Fate File Information for SureSelect Bait Tiling Jobs
- The storage time for design parameters and fate files for SureSelect bait tiling jobs is now six months. This was increased from two weeks and makes it more convenient for researchers to preserve the design parameters for important bait groups.
Increased Maximum Number of Baits that can be Downloaded from SureSelect Bait Search Results
- The limit for the number of baits that can be downloaded from bait search results has been increased to 50,000. Previous versions of eArray limited the maximum number to 10,000 baits.
Improved Packaging of Annotation File Download Archives
- Annotation file downloads are now packaged in a single .zip file archive. There are no longer multiple .zip archives nested within the main .zip archive.
Support for Tab-Text file for GenBank Accession Upload to RNA Enrichment Bait Tiling Wizard
- Users are no longer required to create a .zip archive of their gene list in order to upload it to the bait tiling wizard.
Updated Help and Info Links in the User Interface
- Embedded Help materials in the user interface have been thoroughly reviewed and updated.
21/02/11: Mormor’s Pandekager (Grandma’s Pancake recipe)
February 21, 2012 by Peter · 1 Comment
This post is nothing to do with biotech, life science sales, or my day to day business. It’s just a recipe for pancakes.
As some of you might know, today is Shrove Tuesday, or Pancake Day, in the United Kingdom. Although I am living in Denmark, this is one tradition I still am trying to continue with, especially now I have one daughter and two more on the way…
I’m also posting this recipe because my wife keeps losing it, so I told her that once it was on the internet, it was available for ever. It is her grandmother’s (Mormor’s) recipe for pancakes. Nothing special, but it just works and I hope you try it out:
Enough for 8 people.
500g flour
1 teaspoon salt
2 dessert spoons sugar
1½ L milk
4 eggs
Porridge oats, to taste
Fry in butter
In Danish:
500 gr. mel
1 tsk salt
2 spsk. sukker
1½ L mælk (ca.)
4 æg
Evt. harvegryn
Stejes i smør
That’s it. Available forever, never to be lost!
15/02/12: Agilent Technologies Microarrays Used in Groundbreaking Prenatal Research Study
February 15, 2012 by Peter · Leave a Comment
On Monday, February 13th, Agilent issued a press release (please see it here) announcing the exciting results of a pre-natal collaborative research study conducted by Baylor College of Medicine, Emory University, Columbia University and Signature Genomics. The study was sponsored by the National Institute of Child Health and Human Development (NICHHD). The objective of the study was to evaluate the accuracy and efficacy of using microarrays compared to conventional karyotyping.
15/02/12: Agilent Launch Updated Targeted Enrichment Site
February 15, 2012 by Peter · Leave a Comment
Here: www.agilent.com/genomics/ngs
Lots of new information and a very clear video explaining how HaloPlex technology works. I really needed that!
25/01/12: IDT Launch gBlocks, a Revolutionary New Approach to Gene Synthesis & Alternative to Cloning
January 25, 2012 by Peter · Leave a Comment
I am sooo excited about this new product from IDT. By making genes more affordable, while significantly increasing the speed of delivery, IDT are making synthetic genes more accessible to labs than they have been before.
In short, gBlocks™ Gene Fragments are double-stranded, sequence-verified DNA blocks up to 500 bp in length that can be shipped in 3–4 working days. You define the sequence. Prices are great (EUR 89/DKK 662/ SEK 787), which makes them a realistic alternative to cloning. Users can simply order individual gBlocks, assemble them and drop them straight into their favourite vector.
Anyway, enough from me. If you want to learn some more, please visit the IDT website and try them out!
Update, 27th January:
There are several resources on isothermal assembly, which is one of the recommended methods by which gBlocks can be used to create larger gene fragments. Here is the protocol on the Megason Lab wiki page. The page also contains a link to the original Nature Methods paper, describing the technique.
I wonder if it is just a matter of time before a commercial kit comes out for this…
25/01/12: Agilent Launch Feature Extraction v.11
January 25, 2012 by Peter · Leave a Comment
This should be of interest to all of you who are using an Agilent scanner to scan your microarrays.
Agilent are pleased to announce the launch of the new standalone Feature Extraction version 11. Feature Extraction 11 represents an evolution in Agilent’s standalone software capability and is able to extract data from all Agilent’s microarrays, including CGH+SNP arrays.
Along with Feature Extraction 11 there is the introduction of the new QC Chart Tool v2.0, which is now integrated to Feature Extraction and installed with it.
In addition, the Feature Extraction product page has been updated to include the link to download the new FE 11.
23/01/12: Upcoming Agilent Webinar on “Array CGH and Genomic Medicine in Hematological Malignancies,” Feb. 9th
January 23, 2012 by Peter · Leave a Comment
This looks like an interesting event, because it covers the subject of using aCGH microarrays for cancer in a clinical setting.
The webinar will be run on WebEx and you can learn more/register here.
Event Description
Traditional cytogenetic techniques such as chromosome analysis and FISH have provided valuable genetic information for the evaluation of hematological malignancies. However, many genomic abnormalities remain undetected due to the limitations intrinsic to these techniques. Recently, the introduction of DNA array-based technologies has enabled the identification of previously undetected copy number changes with an increased resolution and sensitivity and a more precise determination of genomic break points and gene content. We have designed and validated a combined targeted-whole genome custom oligonucleotide microarray for the evaluation of hematological malignancies in clinical research. The use of this technology not only allowed us to confirm genetic alterations identified by chromosome analysis or FISH, but also enabled the detection of novel genomic imbalances in myeloid, lymphoid and plasma cell disorders. Several copy number alterations were observed in karyotypically normal patients allowing the discovery of potential tumor suppressor genes or oncogenes important in the pathogenesis of several hematological neoplasms such as myelodysplastic syndrome, multiple myeloma and chronic lymphocytic lymphoma. Our work also emphasizes the importance of incorporating this technology into current algorithms used in clinical cancer research.
20/01/12: Upcoming Conference in Denmark: Integrative Network Biology 2012, 11-13 May 2012
January 20, 2012 by Peter · Leave a Comment
This conference in Denmark looks really interesting for anyone interested in Systems and Network Biology. The organizers have done a great job in getting together a good set of international speakers and it is not too expensive. Plus, May is one of the nicest months to visit Denmark. The conference venue is reasonably close to the nice beach at Snekkersten, if my memory is correct.
Check out the conference homepage here.
The only downside (for me at least) is that I won’t be able to make it!!
17/01/12: Agilent Pre-Conference Workshop at AGBT 2012, February 15th
January 17, 2012 by Peter · Leave a Comment
Sounds pretty good:
Agilent’s Pre-Conference Workshop at AGBT
Wednesday, February 15, 2012 | 9:00 am – 1:00 pm
Save the Date! Register for Agilent’s Pre-Meeting Workshop and be the first to hear about Halo Genomics’ revolutionary products for Next Gen Sequencing. Agilent will be hosting keynote researchers for an in-depth review of cutting-edge research.
Speakers Include:
Edwin Cuppen Ph.D., Hubrecht Institute
Alexander Hoischen Ph.D., Radboud University Medical Centre
Andrew Brown Ph.D., Ontario Institute for Cancer Research (OICR)
John Stamatoyannopoulos Ph.D., University of Washington
John Mcpherson Ph.D., The Ontario Institute for Cancer Research
Somasekar Seshagiri Ph.D., Genentech
And more keynotes TBA!
More details and Registration Here
16/01/12: Agilent miRNA Microarray Product Update: miRBase 18.0 content now available
January 16, 2012 by Peter · Leave a Comment
Agilent have announced that new probes and annotations based on the latest miRBase release 18.0 (http://www.mirbase.org/) are now available in eArray.
Releasing the v18 probes in eArray allows researchers to design a miRNA microarray containing content specific for their experimental needs. In eArray, it is possible to create a custom miRNA design using probes to target any miRNA for any species included in miRBase.
The excellent quality of Agilent’s miRNA arrays, plus the ability to run 6 samples per microarray slide, makes them an excellent choice for miRNA researchers.
16/01/12: Agilent Genomics User Meeting 1st/2nd March 2012, at Sanger Genome Campus
January 16, 2012 by Peter · Leave a Comment
I have just heard that Agilent is organising a Genomics User Meeting to be held at the Wellcome Trust Conference Centre at the Sanger Genome Campus on 1st and 2nd March 2012.
The two days will cover researchers’ entire genomics workflow for microarrays and next generation sequencing and Agilent will be announcing some new product launches during the meeting. Good reasons to go!
The meeting is FREE to attend and will include all meals and refreshments, including a 3 course dinner on the Thursday evening. However you should arrange your own travel and accommodation.
There are a number of hotels available nearby including the Holiday Inn Express in Whittlesford http://www.hiexpresscambridgeduxford.co.uk/ and the Red Lion in Hinxton http://www.redlionhinxton.co.uk/.
Rooms are also available on site at a rate of £88.50 per night including breakfast. To book please call the conference reception on 01223 495000.
Please book as soon as you can as there are only 50 rooms available. The venue provides complementary car parking for all delegates and free wifi in all rooms.
PLEASE NOTE: Places at the meeting are limited so Agilent will be accepting registrations on a first come first served basis. Thank you for your understanding.
Please reply to me through the contact page to register your interest in the meeting and state any special dietary requirements. Also please let me know if you would be interested in presenting your research using Agilent’s genomics solutions during the meeting, in the form of a talk or poster.
11/01/12: Core Center for “Next Generation Sequencing” to Open in Aarhus
January 11, 2012 by Peter · Leave a Comment
In Danish: http://www.auh.dk/presse/nyheder/visnyhed?visNyhed=104792
I know this lab reasonably well. They have lots of equipment in modern labs close to Skejby Hospital. Good luck to them.
11/01/12: Video of Integrated DNA Technologies’ (IDT) European Facility
January 11, 2012 by Peter · Leave a Comment
It is great to be able to find further information on IDT available on the internet. I think that the following will be interesting to a lot of customers who are currently using IDT: A video of the IDT European facility in Leuven, Belgium. The US sites will have a lot of similarities of course. Have you ever wondered what a world-class oligonucleotide synthesis facility looks like? Wonder no more…
02/01/12: Paper Demonstrating Use of SureSelect to Capture Methylated DNA
January 2, 2012 by Peter · Leave a Comment
There was a paper recently published using SureSelect in solution to capture methylated DNA (http://www.ncbi.nlm.nih.gov/pubmed/22151801). It is a nice proof of principle, showing that methylation capture can be performed with SureSelect.
21/12/11: Video of Palm PCR in Action is Now Available
December 21, 2011 by Peter · Leave a Comment
For those of you who are a little curious about the Palm PCR instrument, there is a video demonstration available (see below).
Only problem I have with this vid is that it is a bit long and the changes in speed don’t help. A 7 minute video should also have a bit of music/commentary too. I never thought I would miss “cheesy marketing voice-over man,” but I do!
Still, this video is great because it shows the Palm PCR instrument in operation and gives researchers an idea of how it could be used. It would be cooler if it was shown being used somewhere far away from a lab bench, but maybe that will come later.
15/12/11: Agilent Launch the 2200 TapeStation System
December 15, 2011 by Peter · Leave a Comment
OK, I am way way behind in updating my news section. This particular product was launched about a month ago under the Agilent banner. I’ve already been on a couple of customer demonstrations with it and am very impressed with the ease-of-use and fast sample processing. This is coming from a huge fan of the 2100 Bioanalyzer (which is a brilliant instrument).
There is a short and informative video explaining the TapeStation system on You Tube, which I’ve embedded below. Please take a few minutes to watch it. You’ve gotta love the flying ScreenTapes:
The new Agilent 2200 TapeStation system offers scalable throughput and rapid results, making it an ideal solution for quality control of biological samples in next-generation sequencing (NGS), microrarray and qPCR workflows, as well as in protein purification and antibody production.
The 2200 TapeStation system uses credit card-sized, disposable Agilent ScreenTape that is available for DNA, RNA and protein applications. Sample analysis has never been so easy – simply load the 2200 TapeStation instrument with ScreenTape, loading tips, and your samples in tube strips or 96-well microtiter plates – and you will be reviewing results in approximately 1 minute per sample!
There is a demonstration TapeStation available in the Nordic countries that I can get access to. A demonstration will take about 90 minutes in total (it is really very fast). If you would like a demonstration, or would like to learn more, please contact me.
02/12/11: Agilent Acquires Halo Genomics for DNA Target Enrichment Technology
December 2, 2011 by Peter · Leave a Comment
Wow, it’s been a while since I posted. Organising seminars takes it out of you. Anyway, I heard about this yesterday and think it is a very interesting development.
Agilent’s SureSelect is a great technology, but Halo Genomics’ technology seems to fit a hole in the diagnostic applications field. I already had one customer who tried it out and was happy. This is what Agilent’s press release has to say about Halo Genomic’s technology:
“Halo Genomics’ technology addresses sequence-selective (or “target enrichment”) sample preparation in next-generation sequencing. The company’s proprietary HaloPlex technology combines the speed and specificity of polymerase chain reaction-based systems with the scalability and capture-size flexibility of solution-based hybridization formats, thus eliminating the need for library preparation. This fast and simplified target enrichment solution for next-generation sequencing helps to remove bottlenecks associated with targeted resequencing without the use of expensive, dedicated instrumentation or laborious protocols.
Halo Genomics’ current HaloPlex technology is offered as a customizable product, using a Web-based design tool called Web Design Wizard. This highly intuitive tool enables users to create designs in less than 10 minutes, at no charge.”
Actually, I had heard good things about Halo Genomics software and that this tool looked great for diagnostic sequencing applications.
All-in-all, an acquisition I like.
06/10/11: Scientists, if you are organizing a conference: some tips on getting sponsorship money
October 6, 2011 by Peter · 2 Comments
This post is inspired by a conversation I had earlier this week with a researcher who is trying to get one of the companies I represent to sponsor his conference. If you are thinking of doing something similar, I hope you will find the post useful. The ideas are primarily aimed at someone in a university setting who is hosting a “typical” academic conference, but may well be useful in other circumstances.
Sponsorship from companies is really important for scientific conferences. It often pays for a big part of the costs for hiring the venue, the food, flying in big-name speakers, printing of the abstract book etc. It also helps keep the cost of registration down, so that as many people who are interested can actually attend. Therefore, I am convinced that sponsorship is a big factor in deciding whether a conference is successful or not.
Despite this, I have experienced that many researchers organising scientific conferences seem to treat sponsors – once they’ve got the money - the way they treat a used latex glove: hold with fingertips at arms length and discard quickly. The attitude can be summed up as: “We buy your products (or in some cases ” are thinking about buying”). Please sponsor us. Thank you. We can now spend the next 2 days ignoring your exhibit.”
To be honest, in the past, some companies have gone along with this and might well have contributed to this “easy money, no respect” attitude. I am definitely guilty, making dumb decisions and justifying them with such lame excuses as:
- “Professor Big Name is the organiser (well one of his post-docs in reality). He might finally buy from us if we suck up to him,”
- “Company X are there so we have to be there,”
- “it’s about raising awareness,”
- “I’ve never been to Prague.” (OK, this last one was never stated out loud)
Anyway, my message to you is this: by and large, those days are over. Believe it or not, companies actually want to get something for their money.
I’ll let you into a secret. Companies talk about ROI. It stands for Return On Investment. So, if a company spends $20K on attending a conference, but can only link the sale of one enzyme kit worth $75 back to the conference, that is a “lousy ROI.” Remember, in addition to sponsorship, a company will pay for its employees travel and hotel rooms, shipping of exhibit material, maybe flying in a specialist. All that can actually cost more than the actual sponsorship. Lousy ROI means no sponsorship for you, no more trips to Prague for company reps. Everybody loses out.
How can you, as organiser, ensure that your conference delegates are going to be good for a company’s ROI? Well, actually you can never guarantee that, but that’s OK, because there is something else you should know about ROI: it is actually quite difficult to measure – and many companies don’t measure it, even if they talk about it. You can use this fact to your advantage, because as conference organiser, your job is to think about doing stuff that increases ”potential ROI” and sell that potential to the likely sponsors. If you do a good job on organising with a thought to their ROI, it might well turn into ” real good ROI” for the companies involved. They will be happy and more likely to cough up for your next conference. Nice, eh?
All of the above preamble is to set the scene for a few ideas that you can use to encourage company sponsorship of your conference:
1. Do everything you can to encourage delegates to visit the company exhibits during the conference breaks. Look, we company people know a whole bunch of stuff that you scientists don’t. We know what’s new, what’s upcoming, we know which products are good, we can arrange samples, discounts, instrument demos, tell you which applications are hot and what other researchers are using. Plus, scientists are clever, right? So they are not going to fall for a dumb sales pitch, are they? Therefore, they have great reasons for talking to company representatives without any obligation to spend money.
To get your delegates visiting the exhibits, try these ideas:
- Good location. You have to get researchers in the same room as the exhibitors. That means coffee breaks, buffet lunch and poster sessions should be held in the same room as the exhibits. Obvious? Yes, but you’d be surprised how often this does not happen.
- Set up a prize competition that requires delegates to get information/stamps/whatever from each of the exhibitors. A quiz is a good idea.
- Remind delegates - every now and then - who is paying for a big chunk of the conference. Visiting the exhibits is simply a nice way of being polite and saying “thanks.”
- Make the breaks a decent length. 20 minutes minimum for coffee breaks.
- Allow perhaps one exhibitor to have a stand during the main conference dinner and pay for the privilege. If you put them in charge of the extra wine, their stand will be very popular and they will be very happy.
2. Give out the delegate list after the conference is over. Marketing departments like this (and they normally hold the purse strings for conference spending). You can choose to make this exclusive, a condition of “special, pricier sponsorship,” so that it does not go to all companies. More sponsorship cash for you.
3. Sponsored speaking sessions. Many companies will be happy to bring in a researcher to give a talk about their research that highlights a company technology (usually forming just a small part of the talk). The researcher will have something interesting for the delegates to hear and will not be “salesy” with respect to the technology. Companies appreciate the kudos this gives them and it gives a good chance for interested researchers to visit their exhibit and learn some more. For this reason, consider making these sessions just before breaks.
4. Assign seats at the conference dinner, mixing company people up with delegates. Actually, I think this is generally a good rule for academic-style conferences anyway. Get people out of their comfort zone and mix up PIs with postgrads and postdocs from different parts. After all, a conference should be a networking opportunity for everyone there. That will get the party started.
I believe that if you try out these ideas, in addition to the normal ideas (advertising in abstract, logo placement etc.), you’re sending out the message that you understand what sponsoring companies are after and are willing to work with them. Having an interesting conference program with some big-name speakers is not enough in itself to get companies to sponsor your conference. If you’re successful and get decent sponsorship, you might be able to hold your conference somewhere really nice. Like Prague. I never did get to go in the end.
What do you think? Any additional ideas would be appreciated too.
04/10/11: Information on Agilent’s Autumn Promotions for Genomics Researchers
October 4, 2011 by Peter · Leave a Comment
Agilent are running a bunch of promotions on genomics-related product this Autumn (actually it’s turning out to be the nicest time of year, given the wet Summer). They are summarized here:
- Bioreagents: Buy 3 Stratagene products, get the cheapest one for 1 DKK
- Brilliant III: Buy 1 kit of Brilliant III qPCR reagents, get a second one for free
- Genespring & microarrays: Get 50% off your Genespring data analysis software annual licence when you order > DKK 112K of genomics products
- SureSelect: Buy 1 SureSelect target enrichment kit and get a second one for free (valid for 5 to 25 reaction kits)
- SureCycler bundles: Combine our SureCycler 8800 PCR instrument with our Mx 3005P real-time PCR instrument or with our microchip electrophoresis system (Bioanalyzer 2100 or Lab 901 TapeStation) and get 30% off your bundle
You can also go to the Official Agilent Autumn Promotion page.
Save time by contacting me directly if you are interested.
26/09/11: Symposium on 2nd Generation Sequencing, Copenhagen 28th September 2011
September 26, 2011 by Peter · Leave a Comment
This looks like being a really interesting meeting. Agilent will have an exhibit there, so if you plan on coming along, I hope to meet you.
Symposium on 2nd Generation Sequencing, Wednesday 28th September 2011, Lundbeck Auditorium, Biocenter, Ole Maaloes Vej 5, Copenhagen.
The meeting agenda can be downloaded here.
