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compBiomeBlog | compbiome.com Reviews
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Snippets of Computational Biology, Bioinformatics, Productivity and the like
compbiome.com
compBiomeBlog: R: Using RColorBrewer to colour your figures in R
http://www.compbiome.com/2010/12/r-using-rcolorbrewer-to-colour-your.html
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Wednesday, 8 December 2010. R: Using RColorBrewer to colour your figures in R. RColorBrewer is an R packages that uses the work from http:/ colorbrewer2.org/. RColorBrewer help you to do this. Below is some example R code that generates a few plots, coloured by RColorBrewer. The colours are split into three group, sequential, diverging, and qualitative. Sequential - Light colours for low data, dark for high data. This is great,...
compBiomeBlog: LSF: Using job arrays
http://www.compbiome.com/2010/12/lsf-using-job-arrays.html
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Thursday, 16 December 2010. LSF: Using job arrays. Our cluster uses the LSF. Another benefit of jobs arrays is that they are submitted as a single job, so a job array with a thousand parts is submitted instantly, but submitting a thousand separate jobs would take a long time. Generate a random big file that we want to sort, 10 Million lines. Perl -e 'for (1.1E7){printf("%.0f n",rand()*1E7)};' bigFile. The main point is that the...
compBiomeBlog: Randomize lines in two files, keeping relative order
http://www.compbiome.com/2012/08/randomize-lines-in-two-files-keeping.html
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Thursday, 16 August 2012. Randomize lines in two files, keeping relative order. I recently wanted to randomize the lines in two files, but to keep the relative order of the lines between the files. So I can remember how to do this next time I will post it here. For i in `cat file1.txt`;do echo $RANDOM;done randomOrder.txt. Paste randomOrder.txt file1.txt file2.txt sort -k1n sorted.txt. Cut -f 2 sorted.txt file1.txt.
compBiomeBlog: Perl One Liner: Delete files with wrong number of lines
http://www.compbiome.com/2011/07/perl-one-liner-delete-files-with-wrong.html
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Thursday, 28 July 2011. Perl One Liner: Delete files with wrong number of lines. Just a quick perl one liner for future reference. I needed to delete some text files that didn't have the correct number of lines as they would break a downstream R script to parse the results. For f in *.txt;do perl -ne 'END{unlink $ARGV unless $.= 200}' ${f} ;done. I always forget that $ARGV. Is the variable for the input file name in a one-liner.
compBiomeBlog: Things I would tell a budding bioinformatician to learn.
http://www.compbiome.com/2011/07/things-i-would-tell-budding.html
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Thursday, 7 July 2011. Things I would tell a budding bioinformatician to learn. I recently read Ewan Birney's blog post. 1) Learn a scripting language. 2) Learn a Version Control system. 4) You can't beat a good figure. 5) Learn LaTeX (and Sweave). This point is probably more controversial, as lots of people get a long fine without LaTeX. I started to learn LaTeX as part of learning Sweave. Mality. But impo. 7 July 2011 at 14:53.
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Computational Biology Blog in fasta format: February 2014
http://tata-box-blog.blogspot.com/2014_02_01_archive.html
Computational Biology Blog in fasta format. Tuesday, February 25, 2014. Convert Ensembl, Unigene, Uniprot and RefSeq IDs to Symbol IDs in R using Bioconductor. Hello, I have programmed a function that converts different sources of IDs to Symbol IDs. The input ID types allowed are (at the moment): Ensembl, Unigene, Uniprot and RefSeq. The code is available clicking here. NOTE: The function depends on the Bioconductor package "org.Hs.eg.db" available here. For example, lets show 10 Ensembl IDs:. Then, add ...
Computational Biology Blog in fasta format: August 2014
http://tata-box-blog.blogspot.com/2014_08_01_archive.html
Computational Biology Blog in fasta format. Sunday, August 10, 2014. To cooperate of defect (besides of coding): Prisoners dilemma, a game theory example in R. Hello Computer Science and/or R enthusiasts. This week I had the opportunity to try something that was in my To-Do list a while ago. The idea came almost instantly after reading Dr. Richard Dawkins. Book, The Selfish Gene. Which was a BD gift, thanks Andy). You can download the code here. Similarly, if Blue cooperates while Red defects, then Blue ...
Computational Biology Blog in fasta format: July 2014
http://tata-box-blog.blogspot.com/2014_07_01_archive.html
Computational Biology Blog in fasta format. Monday, July 7, 2014. What are the names of the school principals in Mexico? If your name is Maria, probably this post will interest you. Trends and cool plots from the national education census of Mexico in 2013. I will start this post with a disclaimer:. These trends in data would answer questions such:. 1 Are the most common first names distributed equally among the states? 2 Does the states sharing the same region also share the same "naming" behavior?
Computational Biology Blog in fasta format: To cooperate of defect (besides of coding): Prisoners dilemma, a game theory example in R
http://tata-box-blog.blogspot.com/2014/08/to-cooperate-of-defect-besides-of.html
Computational Biology Blog in fasta format. Sunday, August 10, 2014. To cooperate of defect (besides of coding): Prisoners dilemma, a game theory example in R. Hello Computer Science and/or R enthusiasts. This week I had the opportunity to try something that was in my To-Do list a while ago. The idea came almost instantly after reading Dr. Richard Dawkins. Book, The Selfish Gene. Which was a BD gift, thanks Andy). You can download the code here. Similarly, if Blue cooperates while Red defects, then Blue ...
Computational Biology Blog in fasta format: June 2014
http://tata-box-blog.blogspot.com/2014_06_01_archive.html
Computational Biology Blog in fasta format. Wednesday, June 18, 2014. SOLVED] Problems compiling Rcpp dependent R packages in Crunchbang Linux 11 (Debian 7.5 (wheezy) 64-bit). I had a very weird issue when I tried to compile (install) certain R packages like "wordcloud", "RSNNS" or "GOSemSim" (a Bioconductor package). The installation always ended with a compiling error at the end. In summary, using the default Rprofile.site worked for me. Posted by Benjamin Tovar Cisneros. Subscribe to: Posts (Atom).
Computational Biology Blog in fasta format: What are the names of the school principals in Mexico?, If your name is Maria, probably this post will interest you. Trends and cool plots from the national education census of Mexico in 2013
http://tata-box-blog.blogspot.com/2014/07/what-are-names-of-school-principals-in.html
Computational Biology Blog in fasta format. Monday, July 7, 2014. What are the names of the school principals in Mexico? If your name is Maria, probably this post will interest you. Trends and cool plots from the national education census of Mexico in 2013. I will start this post with a disclaimer:. These trends in data would answer questions such:. 1 Are the most common first names distributed equally among the states? 2 Does the states sharing the same region also share the same "naming" behavior?
Computational Biology Blog in fasta format: December 2012
http://tata-box-blog.blogspot.com/2012_12_01_archive.html
Computational Biology Blog in fasta format. Sunday, December 2, 2012. Póster presentado en la XIV Escuela de Otoño en Biología Matemática, México. Póster presentado en la XIV Escuela de Otoño en Biología Matemática - 8vo Encuentro de Biología Matemática celebrado en San Luis Potosí, S.L.P, México:. Predicción de promotores RNA POL-II en Drosophila melanogaster utilizando propiedades de señal, contexto y estructura a partir de secuencias nucleotídicas". Posted by Benjamin Tovar. S t = eS t-1. The second f...
Computational Biology Blog in fasta format: May 2013
http://tata-box-blog.blogspot.com/2013_05_01_archive.html
Computational Biology Blog in fasta format. Saturday, May 25, 2013. Make your LaTex presentations using the Beamer class. Hello, I have been working with this tutorial. All you need to do is download the source files and take a look at the source code and the PDF file. Hope you find LaTex as useful as I do. Posted by Benjamin Tovar Cisneros. Subscribe to: Posts (Atom). My superpowers are Machine Learning, data analysis and playing guitar. Keep on rocking & programming while awesome = TRUE. Make your LaTe...
Computational Biology Blog in fasta format: UPDATE: 100 Prisoners, 100 lines of code, a game theory example in R
http://tata-box-blog.blogspot.com/2014/08/update-100-prisoners-100-lines-of-code.html
Computational Biology Blog in fasta format. Friday, August 1, 2014. UPDATE: 100 Prisoners, 100 lines of code, a game theory example in R. I was looking for some Game-Theory post in R-bloggers. And found this very cool post. Obviously I decided to read the post, to look at the code and implement a version of it. The idea of the post was very cool for me that I thought it would be a nice idea to get more "juice" from it. All the credit for this post, is for its original author. The code is available here.
Computational Biology Blog in fasta format: October 2013
http://tata-box-blog.blogspot.com/2013_10_01_archive.html
Computational Biology Blog in fasta format. Saturday, October 19, 2013. Optimizing a multivariable function parameters using a random method, genetic algorithm and simulated annealing in R. Say that you are implementing a non-linear regression analysis, which is shortly described by wikipedia. For the training set, we have the following:. And the function to optimize the parameters is:. Which leads us to the following equality:. Given theta (each parameter a0,.a3 has a range from 0 to 15):. MSc in Comput...
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Computational Chemistry and Biochemistry
This site is dedicated to computational chemistry and biochemstry.
The CompBio Dude
Biology from the Computational Point of View. Tuesday, July 28, 2009. More Jython and BioJava. The exploration of how it use BioJava with Jython I've written up an example that takes a Genpept file. An does alignments (both NeedlemanWunsch and SmithWaterman) against every Coding feature in a Genebank file. CDS sequences are kept in the Annotations of Features. If you read the straight sequence from the Genebank file, you will get the DNA of the chromosome. From java.io import *. Column uses minimum score.
The CompBio Experiment
Information Gathering Form End-Users. Information Gathering Form for Expertise Providers. Information Gathering Form for Resource Providers. Information Gathering Form for Software Providers. Technical Computing at Your Fingertips, the next Utility? This is an open invitation to members of the Life Sciences. Community to join us for a 3-month experiment, where we will apply the cloud computing service model to workloads on remote Cluster Computing resources in the areas of bio, pharma, and chemistry.
Richard D. BerlinCenter for Cell Analysis & Modeling › University of Connecticut Health Center
Richard D. Berlin. Center for Cell Analysis and Modeling. 16th Annual Virtual Cell Short Course. June 22-24, 2015. The Richard D. Berlin Center for Cell Analysis and Modeling (CCAM),. At the University of Connecticut Health Center, is developing new approaches for in vivo measurements and manipulation of molecular events within the cell, and new computational approaches to organize such data into quantitative models. Model - develop new methods for spatial modeling of biological systems.
最短で稼げる福岡の出稼ぎ求人
1月 8th, 2015 Author: admin. 1月 8th, 2015 Author: admin. 1月 8th, 2015 Author: admin.
compBiomeBlog
Snippets of Computational Biology, Bioinformatics, Productivity and the like. Thursday, 15 May 2014. Geeknote - Command line interface for Evernote. I have been using Evernote for several years and have been a premium member since 2011 as I was using it so much before then. I use it for work and for home, for recipes and for code, for pretty much everything. I use a modified version of The Secret Weapon. For tracking tasks and priorities. I also use IFTTT. Then I found evernote-mode. For emacs and though...
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CompBiomechBlog
Blog of the Computational Biomechanics Research Group - Using Virtual Reconstruction and Computational Biomechanics to study form and function in biology: Stephen Wroe (Director) email: swroe@une.edu.au phone: 61 2 6773 3261 or 04323 49049. Monday, February 10, 2014. Function Evolution and Anatomy Research (FEAR) Lab. Monday, November 18, 2013. D to report that. My co-CIs and I have recently been awarded over $940,000 in funding from the Australian Research Council. Details below. Total: $339,204.00.
CompBioMed
A Centre of Excellence in Computational Biomedicine. CBK Sci Con Limited. Based on human biology, are now reaching maturity in the biomedical domain, rendering predictive models of health and disease increasingly relevant to clinical practice by providing a personalized aspect to treatment. Computer based modelling and simulation is well established in the physical sciences and engineering, where the use of high performance computing (HPC) is now routine. The project runs for three years from 1. CompBioM...
Computational and Mathematical Biomedical Engineering | CMBE2015
COMPUTATIONAL and MATHEMATICAL BIOMEDICAL ENGINEERING. 4th International Conference on Computational and Mathematical Biomedical Engineering. 29 June - 1 July 2015. Ecole Normale Superieure de Cachan (ENS Cachan) 61 Avenue du President Wilson 94230 Cachan, France. Computational and Mathematical Biomedical Engineering. Abstracts must be prepared as a PDF file using the template provided for electronic submission, consult the Abstract Submission. Please also refer to the CMBE Publishing Policy. Format....
