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Search found 37 results on 2 pages for 'bioinformatics'.

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• How do programmer-seeking employers see Bioinformatics degree?

  - by Max

  I love programming, but I also love biology. Basically Bioinformatics sounds fun to me. However, there is a fat chance that I won't get a Bioinformatics job and will be forced to build my career around regular programming. Therefore a question: does it matter (much) for an employer if he is looking for a regular programmer but finds a…

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• Recommended reading for bioinformatics

  - by Matt

  I'm keen on learning about bioinformatics. I am ideally looking for a short course introduction, with some practical tasks I can get my teeth into immediately to see if there is any interest in it for me. I already have a good understanding of molecular biology, so I should be able to skip most of the foundational work. Any…

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• What do you think is the best language for Bioinformatics?

  - by Ben Fossen

  I have done a couple research jobs in Bio-informatics and I have used Matlab for them. Matlab had a lot of powerful tools and was easy to use. I did thinks with genome sequencing and predicting metabolic pathways. I am wondering what other people think is best? or there might not be one specific language but a few that lend…

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• Bored with CS. What can I study that will make an impact?

  - by Eric Martinez

  So I'm going to an average university, majoring in CS. I haven't learned a damn thing and am in my third year. I've come to be really bored with studying CS. Initially, I was kind of misinformed and thought majoring in CS would make me a good "product creator". I make my money combining programming and business/marketing.…

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• Why is Perl used so extensively in Biology research?

  - by Kevin

  I work as support staff in a Biology research institute as a student, and Perl seems to be used everywhere. Not for every single project, but it seems that more than half the people here have a few Perl books in/on their office/desk. Why is Perl used so much in Biology?

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• A python random function acts differently when assigned to a list or called directly...

  - by Dror Hilman

  I have a python function that randomize a dictionary representing a position specific scoring matrix. for example: mat = { 'A' : [ 0.53, 0.66, 0.67, 0.05, 0.01, 0.86, 0.03, 0.97, 0.33, 0.41, 0.26 ] 'C' : [ 0.14, 0.04, 0.13, 0.92, 0.99, 0.04, 0.94, 0.00, 0.07, 0.23, 0.35 ] 'T' : [ 0.25, 0.07, 0.01,…

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• Is there a Boost (or other common lib) type for matrices with string keys?

  - by mohawkjohn

  I have a dense matrix where the indices correspond to genes. While gene identifiers are often integers, they are not contiguous integers. They could be strings instead, too. I suppose I could use a boost sparse matrix of some sort with integer keys, and it wouldn't matter if they're contiguous. Or would this still…

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• Refining data stored in SQLite - how to join several contacts?

  - by Krab

  Problem background Imagine this problem. You have a water molecule which is in contact with other molecules (if the contact is a hydrogen bond, there can be 4 other molecules around my water). Like in the following picture (A, B, C, D are some other atoms and dots mean the contact). A B . . O / \ H …

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• How can I apply a PSSM efficiently?

  - by flies

  I am fitting for position specific scoring matrices (PSSM aka Position Specific Weight Matrices). The fit I'm using is like simulated annealing, where I the perturb the PSSM, compare the prediction to experiment and accept the change if it improves agreement. This means I apply the PSSM millions of times per…

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• How can I save BioPerl sequence nested features in genbank or embl format?

  - by Ryan Thompson

  In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I…

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• Faster way to split a string and count characters using R?

  - by chrisamiller

  I'm looking for a faster way to calculate GC content for DNA strings read in from a FASTA file. This boils down to taking a string and counting the number of times that the letter 'G' or 'C' appears. I also want to specify the range of characters to consider. I have a working function that is fairly…

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• A graph-based tuple merge?

  - by user1644030

  I have paired values in tuples that are related matches (and technically still in CSV files). Neither of the paired values are necessarily unique. tupleAB = (A####, B###), (A###, B###), (A###, B###)... tupleBC = (B####, C###), (B###, C###), (B###, C###)... tupleAC = (A####, C###), (A###, C###),…

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• Efficient file buffering & scanning methods for large files in python

  - by eblume

  The description of the problem I am having is a bit complicated, and I will err on the side of providing more complete information. For the impatient, here is the briefest way I can summarize it: What is the fastest (least execution time) way to split a text file in to ALL (overlapping)…

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• Parse large XML file w/ script or use BioPython API ?

  - by jeremy04

  Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the…

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• How to generate all strings with d-mismatches, python

  - by mr.M

  I have a following string - "AACCGGTTT" (alphabet is ["A","G","C","T"]). I would like to generate all strings that differ from the original in any two positions i.e. GAGCGGTTT ^ ^ TATCGGTTT ^ ^ How can I do it in Python? I have only brute force solution (it is working): generate…

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• R optimization: How can I avoid a for loop in this situation?

  - by chrisamiller

  I'm trying to do a simple genomic track intersection in R, and running into major performance problems, probably related to my use of for loops. In this situation, I have pre-defined windows at intervals of 100bp and I'm trying to calculate how much of each window is covered by the…

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• Technologies used in EMBL

  - by Sergej Andrejev

  My fried suggest I try to apply for a job at EMBL. I'm not bioinformatic in any way, but my friend (who by the way is a biologist working at EMBL) insists that I could adapt to the new environment as long as I have a interest in subject and am generally good at learning new things. …

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• Java looping through array - Optimization

  - by oudouz

  I've got some Java code that runs quite the expected way, but it's taking some amount of time -some seconds- even if the job is just looping through an array. The input file is a Fasta file as shown in the image below. The file I'm using is 2.9Mo, and there are some other Fasta…

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• How should we serve files in a small bioinformatics cluster?

  - by cespinoza

  We have a small cluster of six ubuntu servers. We run bioinformatics analyses on these clusters. Each analysis takes about 24 hours to complete, each core i7 server can handle 2 at a time, takes as input about 5GB data and outputs about 10-25GB of data. We run dozens of these…

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• Tissue Specific Electrochemical Fingerprinting on the NetBeans Platform

  - by Geertjan

  Proteomics and metalloproteomics are rapidly developing interdisciplinary fields providing enormous amounts of data to be classified, evaluated, and interpreted. Approaches offered by bioinformatics and also by biostatistical data analysis and treatment are therefore becoming…

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• from MS Biology to BS Computer Science [on hold]

  - by Air Borne

  I'm Marco from Italy and I'd like to ask you a piece of advice about my career. I hold a Ms degree in Biology, I enjoyed a lot studying it and I got very good grades but I didn't know what to do with my degree in the real life. Few months ago, I began to read a book about…

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• mpiBLAST: Open-Source Parallel BLAST

  Virginia Tech high-performance computing bioinformatics project reveals missing genes High-performance computing - Parallel computing - United States - Education - Virginia Tech

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• Mandriva Linux is a fantastic scientific platform

  <b>Mandriva Blog: </b>"I'm now a researcher in bioinformatics working as a post-doc on bone cancer. During the past ten years Mandriva has proven rock solid on all the installations I had to perform for my own usage and for my colleagues."

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• best way to go about cost-benefit analysis on hardware

  - by Michael

  I'm looking to build a low-end computational server (my jargon in this field is especially limited so if someone can state that better please change that to meet jargon). I'm basically running computational fluid dynamics programs, large matrix computations and…

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• How to recover unavailable memory in /dev/shm

  - by Alain Labbe

  Good day to all, I have a question regarding the use of /dev/shm. I use it as a temporary folder for large files to speed up processing and save IO off the HD. My problem is that some of my scripts sometimes require "forceful" interruption for a variety of…

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