https://divingintogeneticsandgenomics.com/tags/computation-skills-for-biologist/ Recent content in Computation skills for biologist on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 13 Aug 2015 09:31:00 -0700 https://divingintogeneticsandgenomics.com/archive/2-cents-on-coding-from-a-bioinformatics-beginner/ Thu, 13 Aug 2015 09:31:00 -0700 https://divingintogeneticsandgenomics.com/archive/2-cents-on-coding-from-a-bioinformatics-beginner/ I was trained as a wet biologist and I started learning coding in 2012 April with my first ever python book: python programming for absolute beginners. I still remember the days that after work I would sit down in front of the computer and go through the book until 10pm everyday. It was not that practical in terms of translating what I have learned to what I want to analyze in the lab, but still I have entered into a new world! https://divingintogeneticsandgenomics.com/archive/several-ngs-bioinformatics-training-materials/ Wed, 12 Mar 2014 08:21:00 -0700 https://divingintogeneticsandgenomics.com/archive/several-ngs-bioinformatics-training-materials/ 1. Next Generation sequencing wiki book http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) UCDavis training course https://training.bioinformatics.ucdavis.edu/documentation/ MSU training course by Titus Brown http://ged.msu.edu/angus/index.html GOBLET http://www.mygoblet.org/training-portal  more http://ged.msu.edu/angus/bioinformatics-courses.html a list maintained by Stephen Turner in UVA http://stephenturner.us/edu.html GVL practial protocols for ChIP-seq, RNA-seq, variant calling etc https://genome.edu.au/wiki/GVL These will keep me busy for a while...I feel I do not have enough time to learn :) https://divingintogeneticsandgenomics.com/archive/so-you-want-to-be-a-computational-biologist/ Mon, 11 Nov 2013 09:33:00 -0800 https://divingintogeneticsandgenomics.com/archive/so-you-want-to-be-a-computational-biologist/ See a commentary here : http://www.nature.com/nbt/journal/v31/n11/abs/nbt.2740.html Quotes from the article: “Laboratory scientists wouldn’t dream of running experiments without the necessary positive and negative controls... tests are the computational biology equivalent.” “Knowledge of biology is vital in the interpretation of computational results.” Learning resources: https://divingintogeneticsandgenomics.com/archive/python-code-for-getting-the-reverse-complement-dna-strand/ Thu, 31 Oct 2013 12:58:00 -0700 https://divingintogeneticsandgenomics.com/archive/python-code-for-getting-the-reverse-complement-dna-strand/ Following pythonforbiologist http://pythonforbiologists.com/index.php/business-card-solutions/, I wrote a very simple python script to get the reverse complement DNA strand: View this gist on GitHub It is a very simple script but several things I want to mention: 1. what is the fast string concatenation method in python? in the first function, we tend to write something like: out_seq = ' ' for base in reversed(seq): out_seq += seq_dict[base] but it turned out to be very slow. https://divingintogeneticsandgenomics.com/archive/useful-unix-one-liners-for-bioinformatics/ Thu, 24 Oct 2013 11:23:00 -0700 https://divingintogeneticsandgenomics.com/archive/useful-unix-one-liners-for-bioinformatics/ I have been using ubuntu 12.04LTS for one year, and I really love it and do not look back at windows at all. Currently, I have dual booting system for linux and windows, but now I barely fire the windows. The power of Linux comes from, at least in one aspect, its command line. As I have stated before, in the field of bioinformatics, we spend a lot of time in reformatting, cleaning, extracting the data. https://divingintogeneticsandgenomics.com/archive/a-beginners-guide-to-bioinformatics-fwd-homologus/ Fri, 11 Oct 2013 14:46:00 -0700 https://divingintogeneticsandgenomics.com/archive/a-beginners-guide-to-bioinformatics-fwd-homologus/ See the posts here http://www.homolog.us/blogs/blog/2011/07/22/a-beginners-guide-to-bioinformatics-part-i/ and here http://www.homolog.us/blogs/blog/2011/07/22/a-beginners-guide-to-bioinformatics-part-ii/ 5 layers of expertise in bioinformatics were mentioned: "Layer 1 – Using web to analyze biological data Layer 2 – Ability to install and run new programs Layer 3 – Writing own scripts for analysis in PERL, python or R Layer 4 – High level coding in C/C++/Java for implementing existing algorithms or modifying existing codes for new functionality Layer 5 – Thinking mathematically, developing own algorithms and implementing in C/C++/Java" https://divingintogeneticsandgenomics.com/archive/does-every-new-biology-phd-student-need-to-learn-how-to-program/ Tue, 08 Oct 2013 11:59:00 -0700 https://divingintogeneticsandgenomics.com/archive/does-every-new-biology-phd-student-need-to-learn-how-to-program/ The answer is Yes! see the paper from Nature Biotech http://www.nature.com/nbt/journal/v31/n10/box/nbt.2721_BX1.html " Box 1: Does every new biology PhD student need to learn how to program? Durbin: That's a little like asking is it good for a molecular biologist to know chemistry. I would say that computation is now as important to biology as chemistry is. Both are useful background knowledge. Data manipulation and use of information are part of the technology of biology research now. https://divingintogeneticsandgenomics.com/archive/computational-competence-for-biologists/ Wed, 17 Jul 2013 14:20:00 -0700 https://divingintogeneticsandgenomics.com/archive/computational-competence-for-biologists/ After reading this post http://software-carpentry.org/blog/2013/07/computational-competence-for-biologists.html, I realized that I am far from being competent.... currently, I know some python, R(bioconductor), linux commands, sed, awk, galaxy and feel comfortable to use command line based software like bedtools, samtools, bowtie etc. I still need to enhance my database skills though. More importantly, I will need to have some statistics knowledge. I signed up for Mathematical Biostatistics Boot Camp 1 on coursera https://divingintogeneticsandgenomics.com/archive/yes-you-need-to-validate-the-genomic-discoveries/ Fri, 12 Jul 2013 10:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/yes-you-need-to-validate-the-genomic-discoveries/ I just came back from San Diego, CA. It is a beautiful place, and I enjoyed the staying there very much. well, as the title stated, we need to experimentally validate the genomic discoveries, as more and more NGS studies only focus on bioinformatic analysis of the large data but do not have access to facilities to validate the claimed conclusions. I am switching from a bench worker to a desktop worker, but I still enjoy doing experiment and the techniques I've learned from the wet lab will serve the purpose of validating the hypothesis generated by large data mining. https://divingintogeneticsandgenomics.com/archive/my-personal-suggestions-to-get-started-with-bioinformatics/ Sat, 08 Jun 2013 19:45:00 -0700 https://divingintogeneticsandgenomics.com/archive/my-personal-suggestions-to-get-started-with-bioinformatics/ updated 07/20/13 see a post by Nick Loman http://pathogenomics.bham.ac.uk/blog/2013/07/i-want-to-learn-bioinformatics-a-guide-for-complete-beginners/ I am following him on twitter, and I am glad I knew most points mentioned in the article above. another blog by Titus Brown the author of h-kmer http://ivory.idyll.org/blog/2013-sesync-meeting.html I started doing bioinformatics ( bioinformatics is really a deep river, it may not sound I am doing any real bioinformatics to many bioinformaticians) last year in April. The past one year has been tremendously exciting as I learn new stuff every day and become more confident with huge data analysis. https://divingintogeneticsandgenomics.com/archive/encouraging-how-i-taught-myself-to-code-in-eight-weeks/ Fri, 07 Jun 2013 19:58:00 -0700 https://divingintogeneticsandgenomics.com/archive/encouraging-how-i-taught-myself-to-code-in-eight-weeks/ http://lifehacker.com/how-i-taught-myself-to-code-in-eight-weeks-511615189?utm_campaign=socialflow_lifehacker_twitter&utm_source=lifehacker_twitter&utm_medium=socialflow How I Taught Myself to Code in Eight Weeks To a lot of non-developers, learning to code seems like an impossibly daunting task. However, thanks to a number of great resources that have recently been put online for free— teaching yourself to code has never been easier. I started learning to code earlier this year and can say from experience that learning enough to build your own prototype is not as hard as it seems. https://divingintogeneticsandgenomics.com/archive/how-to-stay-the-current-of-bioinformatics/ Thu, 16 May 2013 07:54:00 -0700 https://divingintogeneticsandgenomics.com/archive/how-to-stay-the-current-of-bioinformatics/ See the post here http://gettinggeneticsdone.blogspot.com/2012/05/how-to-stay-current-in.html How to Stay Current in Bioinformatics/Genomics A few folks have asked me how I get my news and stay on top of what's going on in my field, so I thought I'd share my strategy. With so many sources of information begging for your attention, the difficulty is not necessarily finding what's interesting, but filtering out what isn't. What you *don't* read is just as important as what you do, so when it comes to things like RSS, Twitter, and especially e-mail, it's essential to filter out sources where the content consistently fails to be relevant or capture your interest. https://divingintogeneticsandgenomics.com/archive/bioinformatics-resources/ Wed, 03 Apr 2013 08:42:00 -0700 https://divingintogeneticsandgenomics.com/archive/bioinformatics-resources/ operation system: google Bio-liunx you will find it and you can install it for free. If you use mac, you may consider to have a dual booting system or use a virtual machine. http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info websites: GUI informatics tools:(non-programmers) Galaxy http://galaxyproject.org/ ChIP-seq tools based on Galaxy developed by shirley Liu in harvard Cisgenome http://cistrome.dfci.harvard.edu/Cistrome/Cistrome_Project.html Genome space http://www.genomespace.org/ if you really do not want to learn how to program, use it.