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In between lines of code | Biology, sequencing, bioinformatics and more | flxlexblog.wordpress.com Reviews
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In between lines of code | Biology, sequencing, bioinformatics and more | Page 2
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In between lines of code. Biology, sequencing, bioinformatics and more. Newer posts →. Active learning strategies for bioinformatics teaching. August 31, 2015. The more I read about how active learning techniques improve student learning, the more I am inclined to try out such techniques in my own teaching and training. I attended the third week of Titus Brown’s “NGS Analysis Workshop”. I highly recommended reading it and checking out the references mentioned. I am by no means an expert in the area, ...
Developments in high throughput sequencing – June 2015 edition | In between lines of code
https://flxlexblog.wordpress.com/2015/06/17/developments-in-high-throughput-sequencing-june-2015-edition
In between lines of code. Biology, sequencing, bioinformatics and more. Developments in high throughput sequencing June 2015 edition. June 17, 2015. This is the fourth edition of this visualisation, previous editions were in June 2014. As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale. Yes, I know a certain new instrument seems to be missing, hang on, I’m coming back to that…. Note how close to...
Make Newbler open source | In between lines of code
https://flxlexblog.wordpress.com/2014/01/31/make-newbler-open-source
In between lines of code. Biology, sequencing, bioinformatics and more. Make Newbler open source. January 31, 2014. Cross-posted at contig.wordpress.com. Typical Newbler assembly output. The Newbler assembler and mapper (gsAssembler, gsMapper) was developed especially for working with the reads from the Roche/454 Life Science sequencing technology. It is one of the best programs to deal with this type of data, scoring well in the assemblathon 2 competition. That Roche/454 does not want to make the source...
Ion Torrent Mate Pairs and a single scaffold for E coli K12 substr. MG1655 | In between lines of code
https://flxlexblog.wordpress.com/2012/03/02/ion-torrent-mate-pairs-and-a-single-scaffold-for-e-coli-k12-substr-mg1655
In between lines of code. Biology, sequencing, bioinformatics and more. Ion Torrent Mate Pairs and a single scaffold for E coli K12 substr. MG1655. March 2, 2012. The impatient reader might want to skip to the conclusion at the end of this post…). Last wednesday, Ion Torrent released a tech note. And associated run data. After extracting the pair halves, I adjusted the files so that newbler would accept them as mate pairs, and performed mapping using newbler (gsMapping/runMapping program). Then I plo...
On assembly uncertainty (inspired by the Assemblathon2 debate) | In between lines of code
https://flxlexblog.wordpress.com/2013/02/26/on-assembly-uncertainty-inspired-by-the-assemblathon2-debate
In between lines of code. Biology, sequencing, bioinformatics and more. On assembly uncertainty (inspired by the Assemblathon2 debate). February 26, 2013. The release of the assemblathon2 paper via arXiv. By Titus Brown and his posting of his review. Of the paper sparked a discussion in the comments section of Titus’ blog, as well as on the homolog us blog. With this blog post, I’d like to chip in with a few remarks of my own. 8230;] each assembly is a computational hypothesis, developed from noisy data ...
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Next Generation Technologist - Page 2 of 15 - Next Generation Sequencing, Marketing, and the Genomic Revolution
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Next Generation Sequencing, Marketing, and the Genomic Revolution. Next Generation Sequencing, Marketing, and the Genomic Revolution. Fundamentals of Next Generation Sequencing. One door opens, and another door closes. Highlights from the American Association for Cancer Research Meeting, Philadelphia 2015 #AACR15. Complete human diplotypes & Google X Life Sciences podcast. Theral Timpson produces a weekly podcast at Mendelspod.com, and in his latest edition he interviews me about Google X Life Scienc...
The one where I went to Sweden | The Devil in the Details
https://blog.karinlag.no/2014/06/sweden
The Devil in the Details. The one where I went to Sweden. I spent some days two weeks ago in Stockholm, Sweden. Lex Nederbragt. And I were invited by SciLifeLab. To teach a Software Carpentry. Workshop there. This coincided with the very first PyCon Sweden Conference. And as the organizers would have it, I got to present a talk. The workshop went very well. Lex and I taught the by-now fairly well known novice workshop. If you want one at your institution, let them know. The conference and my talk. Speaki...
Annotate: A Plugin for the Ion Torrent Browser | BioLektures
https://biolektures.wordpress.com/2011/12/29/annotate-a-plugin-for-the-ion-torrent-browser
This blog contains mainly bioinformatics analysis and discussion. Signal Processing – Room for improvements? Are MiSeq miscalls influenced by preceding homopolymers? Annotate: A Plugin for the Ion Torrent Browser. December 29, 2011. Novel versus Common Variants. Stored on the Torrent Server is ordered different to the dbSNP VCF file. From the GATK 1.2 resouce bundle. For this plugin, I have decided to index the VCF file using tabix. And call the variants outside the GATK framework. Functional Impact of N...
Ion Torrent – Rapid Software Improvements | BioLektures
https://biolektures.wordpress.com/2011/09/19/ion-torrent-rapid-software-improvements
This blog contains mainly bioinformatics analysis and discussion. The Ion Torrent Accuracy Challenge – A non-biological explanation. Ion Torrent and the Democratization of Sequencing →. Ion Torrent – Rapid Software Improvements. September 19, 2011. There are three major areas that software can improve. Throughput – Identify more Ion Sphere Particles (ISPs) with library fragments therefore increasing the total number of reads. Quality – More and longer reads aligning back to the reference sequence. The ta...
Life Grand Challenges – Innocentive but not enough Incentives (Part 3) | BioLektures
https://biolektures.wordpress.com/2011/08/18/life-grand-challenges-–-innocentive-but-not-enough-incentives-part-3
This blog contains mainly bioinformatics analysis and discussion. Life Grand Challenges Mission Impossible to Improbable (Part 2). Challenges in Improving Ion Torrent Raw Accuracy (Part 3) →. Life Grand Challenges Innocentive but not enough Incentives (Part 3). August 18, 2011. Ever used IMDB or Rotten Tomatoes as an indicator of how good a movie is and whether you should watch it? While Tekken best movie ever only got 5.0 on IMDB. Competition was open in 2006 and would end in 2011. A progress prize of 5...
Disclaimer | BioLektures
https://biolektures.wordpress.com/disclaimer
This blog contains mainly bioinformatics analysis and discussion. My thoughts, opinions and random outburst are independent and do not reflect the views of the University of Sydney or the Institute for Neuroscience and Muscle Research. In fact, most people in my lab thinks I’m nuts and my jokes are terrible. I have received free dinner! Unfortunately, the Illumina free dinner at ASHG 2011 was invite only😦. Here are the parties I have received food from and my ratings out of 10. Other Mum’s (10/10)...
Are MiSeq miscalls influenced by preceding homopolymers? | BioLektures
https://biolektures.wordpress.com/2012/02/01/are-miseq-miscalls-influenced-by-preceding-homopolymers
This blog contains mainly bioinformatics analysis and discussion. Annotate: A Plugin for the Ion Torrent Browser. Crowd Sourcing 2.0 – Smaller and Faster = Better →. Are MiSeq miscalls influenced by preceding homopolymers? February 1, 2012. A recent post in the Ion Community Torrent Dev section presents an analysis showing MiSeq systematic substitution errors which appear to be caused by preceding homopolymers (HPs). The Omics Omics blog post. 2) E coli MG1655. From a recent Genome Biology publication.
Fundamentals of base calling (Part 1) | BioLektures
https://biolektures.wordpress.com/2011/08/10/fundamentals-of-base-calling-part-1
This blog contains mainly bioinformatics analysis and discussion. Fundamentals of base calling (Prequel). Fundamentals of base calling (Part 2) →. Fundamentals of base calling (Part 1). August 10, 2011. The Ionogram of a well containing. These are raw values extracted from the 1.wells file. Note: The flow order does not follow a repeating 4 flow cycle of T. Packages to produce the plots. The Ionogram of the same well containing. Below are the bases called for this well. This was the 5th best. As this bet...
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In between lines of code | Biology, sequencing, bioinformatics and more
In between lines of code. Biology, sequencing, bioinformatics and more. Experiences with the first edition of “Introduction to Computational Modelling for the Biosciences”. December 21, 2017. Earlier this year, I wrote a post. About the new first-semester bachelor course Introduction to Computational Modelling for the Biosciences at our institute. A quick summary:. From 2017, the Biosciences bachelor study program will incorporate Computing in Science Education (CSE). Into the different subjects. A typic...
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