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MerenLabOn microbial ecology, and bioinformatics
http://www.merenlab.org/
On microbial ecology, and bioinformatics
http://www.merenlab.org/
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On microbial ecology, and bioinformatics
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Software – Meren Lab
http://merenlab.org/projects
For details, and the codebase. To follow the development and/or participate. Is a human-guided computational approach that makes it possible to decompose very closely related taxa at one nucleotide resolution. It is generally applied to the high-throughput sequencing of bacterial marker gene amplicons amplified from environmental samples (such as 16S rRNA gene). See the project page. A metagenomic short read filtering software that uses a flexible configuration format. It allows users to define a cha...
Removing contaminants from cultivars with anvi'o – Meren Lab
http://merenlab.org/2015/06/25/screening-cultivars
Removing contaminants from cultivars with anvi'o. Accessing genomic contamination levels is important, but not enough. Using anvi’o to screen for possible contaminants and to curate individual genomes. Example 1: axenic, uncontaminated culture. Example 2: non-axenic culture of 3 distinct bacterial populations. When Is a Microbial Culture Pure? Controlling for contamination in re-sequencing studies. Microbiome science threatened by contamination. By Connor Skennerton describe some key pitfalls. Using anvi...
Analyzing single nucleotide variations (SNVs) with anvi'o – Meren Lab
http://merenlab.org/2015/07/20/analyzing-variability
Analyzing single nucleotide variations (SNVs) with anvi'o. A Murat Eren (Meren). This is more of a theoretical tutorial. For a more practical one on the same topic, please visit http:/ merenlab.org/tutorials/infant-gut/#profiling-snvs-in-a-bin. Characterization and reporting of SNVs. Generating a SNV profile. Parameters to filter the output. We use the term microbial clouds. Makes it somewhat irrelevant to microbiology). The heterogeneity of the microbial cloud,. And/or the stringency of mapping. Charact...
Comparing different mapping software using anvi'o – Meren Lab
http://merenlab.org/2015/06/23/comparing-different-mapping-software
Comparing different mapping software using anvi'o. A Murat Eren (Meren). A quick first look and initial binning. Number of mapped reads by each mapper. Comparing individual mapping results. Putting all mapping results together. During our discussions to identify which mapping software should we use to map short metagenomic reads to contigs, Bing Ma. But beyond our preliminary findings on the performance of these mapping software, this little project gives a good idea about how versatile anvi’o. HUZ63 is ...
An analysis and visualization platform for 'omics data – Meren Lab
http://merenlab.org/projects/anvio
Anvi’o in a nutshell. Anvi’o is an analysis and visualization platform for ‘omics data. It brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Please see the Tutorials. Pull-down menu on this page for some example workflows with anvi’o. Anvi’o is a community-driven, GPL-licensed open-source project. You can browse its codebase by clicking here. And you can find our methods paper for anvi’o by clicking here.
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How to …. Newer posts →. Phenotypes in Comparative Phylogeography. 11 August, 2016. Earlier this week, The Molecular Ecologist contributor Bryan McLean. Posted about the current state of comparative phylogeography. He listed several exciting directions that comparative phylogeography is heading, including more research that includes trait data. But disregarding discordance may not always be beneficial or appropriate. A biogeographic barrier may influence multiple species, but to varying degrees depen...
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Merenkurkun Lintutieteellinen Yhdistys r.y. Merenkurkun Lintutieteellisen Yhdistyksen säännöt. 103 pöllöretki Iskmossa. Tapaaminen klo 18:30 Gerbyn S-Marketin parkkipaikalla. Ota taskulamppu mukaan, jos mahdollista! HUOM: huonolla säällä, esim. kovalla pakkasella/tuulella retki peruuntuu/siirtyy. Yhteyshenkilö: Hanna Mikkola, hanna.mikkola(a)gmail.com, p.0408451412 […]. Ekaekaa 2018 pinnarallin tulokset. Lokakuun säät olivat varsin vaihtelevat. Enimmäkseen tuulista, keskiarvoa sateisempaa ja keikenka...
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Merenkurkun Noutajat ry - Kvarkens Retrievers rf. WT-treeniä Pohjanmaa Cuppiin osallistuville. TOKON JATKOKURSSI: KOHTI KOETTA. Yhdistyksen vuosikokous 21.3.2018. Rodunomaisten lajien koulutusta 7.-8.4 kouluttajana Maarit Nikkanen. 2018 Merenkurkun Noutajat ry Kvarkens Retrievers rf.
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Måndag 3 augusti 2015. 237 gjordes årets elfiske av föreningen/ Sähkökalastus 2015. Jaakko Muurimäki, Anders Berg och Pekka Mäkynen ( Foto). Efter förra årets goda resultat var förväntningen stor. Hade ändå misstankar om att kläckningen hade gått sämre i år eftersom det fanns mycket öringrom kvar i boxarna då vi tog upp dom i slutet av maj. Visade sig ganska snart att elfisket bara gav abborre och gädda. Orsakerna varför kläckningen inte. Voimme vain arvailla. V. 2014 kokemukset osoittivat kuiten...Proje...
MerenLab
Microbial ecology, bioinformatics, visualization. From the human oral cavity to pristine soils, we. Use our expertise in microbiology and computation to study microbial communities and their ecology. We strive to create. Advanced software platfroms, and design appropriate experiments to contribute. A wide range of concurrent research questions. In the domain of microbial ecology. We are currently located at the Marine Biological Laboratory. Recent posts from the blog. Analyzing variability with anvi'o.
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Understanding the miracle of life using code. Hi, I’m Oxana. Data Scientist, Computational Biologist and Entrepreneur. First an foremost, I’m an Engineer though. That’s my initial training and my way of life. That means I’m solving problems and coming up with creative solutions. I particularly enjoy doing it for science and data visualization, but sometimes also do it as a digital project manager and teacher. When I’m not coding or reading about proteins and DNA, I teach swimming( check out SSIF.
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