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Bits and Bugs | Applying bioinformatics to public health microbiology | bitsandbugs.org Reviews
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Applying bioinformatics to public health microbiology
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Using GATK to call indels in bacterial genomes | Bits and Bugs
https://bitsandbugs.org/2015/04/23/using-gatk-to-call-indels-in-bacterial-genomes
Applying bioinformatics to public health microbiology. Using GATK to call indels in bacterial genomes. April 23, 2015. If you are interested in calling indels with GATK, check out the below. If not, don’t. 8212;—————————————————–. 1 Have a sorted bam file. 2 Run GATK (v.2.6.5 in my case), with the following command. Java -Xmx4g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -nt 1 -R reference.fa -I sorted.bam -o indel.vcf -glm INDELS. 2a I investigated the GATK realigner around indels. As these will be ca...
PhD viva advice | Bits and Bugs
https://bitsandbugs.org/2014/12/30/phd-viva-advice
Applying bioinformatics to public health microbiology. December 30, 2014. I was just asked for some advice on PhD viva, so have turned the email into a blog post. 8212;—————. They often start by asking you to place your work into context of existing literature and summarise your main findings in 5-10 minutes, so have your summary ready. In terms of new articles, I only discussed ones that were directly relevant to my work, they were happy with that. As long as you seem to be aware of other organisms ...
Thoughts on bioinformatics as wet-lab kits | Bits and Bugs
https://bitsandbugs.org/2014/11/02/thoughts-on-bioinformatics-as-wet-lab-kits
Applying bioinformatics to public health microbiology. Thoughts on bioinformatics as wet-lab kits. November 2, 2014. I have just read Sean Eddy’s thought provoking blog post. On the problems with how biology is handling high throughput sequencing which you should definitely read. Nick Loman tweeted an excerpt from Sean’s blog post saying something along the lines of ‘bioinformatics should be more like kits’, I have to admit my first thought was ‘ugh, no! 1) Tool installation. Bioinformaticians often ...
December | 2014 | Bits and Bugs
https://bitsandbugs.org/2014/12
Applying bioinformatics to public health microbiology. Monthly Archives: December 2014. I was just asked for some advice on PhD viva, so have turned the email into a blog post. —————— They often start by asking you to place your work into context of existing literature and summarise your main findings in 5-10 minutes, so have your summary ready. The main prep I did was to…. December 30, 2014. December 30, 2014. Lighter: better, faster, longer? December 11, 2014. Lauren Cowley is currently in Sierra Leone...
November | 2014 | Bits and Bugs
https://bitsandbugs.org/2014/11
Applying bioinformatics to public health microbiology. Monthly Archives: November 2014. Annotating phylogenetic trees with gene presence/absence etc. As a bioinformatician, I spend a lot of time generating, interpreting and presenting trees. One of the most powerful ways to get some added value out of a tree is to be able to compare the phylogeny with the accessory gene content, to see if there is something going on with the mobile genetic elements that…. November 4, 2014. November 2, 2014.
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Teaching Materials |
http://www.langmead-lab.org/teaching-materials
LANGMEAD LAB @ JHU. LANGMEAD LAB @ JHU. You are free to use these materials. If you do, please sign the guestbook at the bottom of this page and say briefly how you’re using them. Algorithms for DNA Sequencing. 55 lectures, about 7 minutes each). Suffix tries and suffix trees. Lecture notes and IPython/Jupyter notebooks. What are Genomics and Computational Genomics? Strings and exact matching. Notebook: Strings in Python. Notebook: Naive exact matching. Notebook: Naive approximate matching. Genes and gen...
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Australian Butterfly and Insects. FREE SHIPPING AUSTRALIA WIDE. BITS and BUGS FRAMED BUTTERFLIES AND INSECTS. WALL DECOR THAT IS. INSPIRATIONAL, EXQUISITE AND SPECTACULARLY BEAUTIFUL. Visitors are welcome to browse the shelves at our warehouse located on the Gold Coast QLD.With over 500 different specialty frames to choose from there’s something for everyone. To arrange a time to suit. Real Papilio ulysses butterfly wing in bottle. Butterfly combo x 6. Mini frame Heliconius telesiphe.
Bits & Bugs | Infectious Disease, Public Health & Health IT
Infectious Disease, Public Health and Health IT. The 2013 influenza season is well underway with most of the United States reporting a greater than average volume at most hospitals. Many of those seeking medical attention are doing so with Influenza like symptoms. I have compiled a list of FAQs that have recently come up:. Continue reading →. This entry was posted in Infections. And tagged infection control. January 13, 2013. Undervaccinated student at California University leads to Mumps outbreak. This ...
Bits and Bugs | Applying bioinformatics to public health microbiology
Applying bioinformatics to public health microbiology. Programatically accessing internal nodes of a phylogeny. This post belongs in the ‘write it down before you forget’ category. Edit – this approach is necessary for handling the trees produced by RAxML, but not those produced by IQ-TREE. Edit #2 – Ancestral state reconstruction in RAxML does not seem to work very well. I’m trying IQ-TREE (v1.6) instead. I have a tree…. Continue reading →. Salmonella genomic epidemiology exercise. Trimmomatic: A flexib...
Bits & Bugs | Infectious diseases in a web 2.0 world
Infectious diseases in a web 2.0 world. MedPage Today News: Single-Shot Skin Antibiotic Passes Hurdle. Posted December 26, 2012 by irfanhafiz. Single-Shot Skin Antibiotic Passes Hurdle. Click http:/ www.medpagetoday.com/Dermatology/GeneralDermatology/36559. For the full story:. Be the first to comment. Identifying false scientific claims. Posted November 12, 2012 by irfanhafiz. I found this article in a recent issue of Forbes. Utm campaign=forbestwittersf&utm source=twitter&utm medium=social. Clostrdium ...
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Bits & Bumps | Obstetrics and Gynaecology FOAM
O&G FOAM and SoMe. Obstetrics and Gynaecology FOAM. July 17, 2015. B&B Basics: The Gynaecological Examination. Http:/ traffic.libsyn.com/bitsandbumps/Gynae exams.mp3. In this episode we go back to the basics with a chat about gynaecological exams. This is one for the students, junior doctors or those that feel their speculum exams are less than spec-tacular. We discuss issues such as:. The use of chaperones for intimate examinations. Patient positioning for success. How to wield the speculum. We’re...
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Upgrade to paid account and never see ads again! 11:42 pm December 31st, 2025. Leave me a feedback. Simply because i care. Simply leave a comment in this format:. Thanks for your time! Or Leave a comment. 10:09 am September 2nd, 2011. Since I'm just 2 weeks plus from leaving, I decided to summarize the food I had while I was working here at Alps. 1- mixed rice stall. 2- handmade noodles stall. 5-1 of the 3 malay stalls. I only eat this when I got no other choice. 3 standard liao I order, long beans, ...
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