Moderator: Simon Cockell

gravatar for Simon Cockell
Simon Cockell7.2k
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Location:
Newcastle
Website:
http://sjcockell.me/
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Last seen:
3 months, 2 weeks ago
Joined:
7 years, 9 months ago
Email:
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Bioinformatician, support scientist, Python programmer. Full bio on my blog. You can also follow me on Twitter.

I run the Bioinformatics Support Unit at Newcastle University.

Posts by Simon Cockell

<prev • 179 results • page 1 of 18 • next >
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Job: Cancer Bioinformatician. Newcastle University, UK.
... Closing date: 21st April 2017. The Newcastle University Bioinformatics Support Unit is seeking to hire a motivated, independent bioinformatician to support active research programmes in the Northern Institute of Cancer Research. The successful applicant will join a large and successful team of sup ...
core facility job cancer written 7 months ago by Simon Cockell7.2k
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Comment: C: How to avoid conversion of gene symbols to date format in Excel
... I admire your idealism @harold.smith.tarheel, but >10 years of experience has taught me that this will not work. You'll pry Excel from their cold, dead hands. ...
written 14 months ago by Simon Cockell7.2k
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Comment: C: How to avoid conversion of gene symbols to date format in Excel
... I would argue that for most, Excel is unfortunately unavoidable - yes, *you* can personally avoid it, but as soon as you send your tab-delimited table to someone else to look at - science is collaborative after all - *they* will open it in Excel. The mangling of gene names by Excel is an entirely ...
written 14 months ago by Simon Cockell7.2k
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Answer: A: How to avoid conversion of gene symbols to date format in Excel
... If we assume that Excel is an unavoidable evil (and for most this is unfortunately a credible assumption)... When importing your delimited data into Excel, be sure to set the column type appropriately. The default for all columns is 'General' - this will lead to the inevitable auto-correct mangling ...
written 14 months ago by Simon Cockell7.2k
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Answer: A: How to identify every read in a fastq file?
... This would seem like a good use case for something like Kraken: But your ability to assign *every* read in your experiment to an organism of origin will depend entirely on the completeness of your database. ...
written 14 months ago by Simon Cockell7.2k
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Comment: C: What is the appropriate approach for ChIPseq protein genome occupancy % calculat
... If the pie chart you're after is like the ones shown in the link provided in Ido's answer below, then I am not mistaken. It is perfectly possible for a ChIP region to be both in a promoter of one gene, and downstream of another gene - so the data are not categorical & a pie chart is wrong. Just ...
written 2.4 years ago by Simon Cockell7.2k
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Comment: C: What is the appropriate approach for ChIPseq protein genome occupancy % calculat
... Your data are not categorical (a occupancy site could intersect with many genomic features) - so a pie chart (rarely the right approach) is definitively wrong here.  ...
written 2.4 years ago by Simon Cockell7.2k
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Job: Two Positions in Bioinformatics Core Facility, Newcastle, UK
... The Newcastle University Bioinformatics Support Unit (BSU) has an 9-year history of supporting cutting-edge research in the Faculty of Medical Sciences. We currently have two open vacancies to join our successful team. One will be based full time in the BSU, dealing with core support requests from ...
bioinformatics jobs job written 3.2 years ago by Simon Cockell7.2k
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News: Command Line Bioinformatics and High-throughput Sequencing Analysis Course
... Short course on the Linux Command Line and analysis of NGS data. Full details at http://bsu.ncl.ac.uk/support/courses/ Newcastle University, UK 17th – 19th November 2014 Many powerful bioinformatics applications do not come packaged with an easy-to-use graphical user interface. Since many people ...
news course training written 3.2 years ago by Simon Cockell7.2k • updated 3.2 years ago by sgr.mdreid0
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Job: Core Facility Positions At Newcastle University, Uk
... The Newcastle University Bioinformatics Support Unit (BSU) has an 8-year history of supporting cutting-edge research in the Faculty of Medical Sciences. As part of a significant investment in bioinformatics by the Faculty, the unit is expanding to help meet the demands of vastly increased high throu ...
bioinformatics jobs job written 4.2 years ago by Simon Cockell7.2k

Latest awards to Simon Cockell

Popular Question 11 months ago, created a question with more than 1,000 views. For How To Find Sequences For Protein Names (A Challenge)
Appreciated 14 months ago, created a post with more than 5 votes. For A: Manipulate Sequences In Fastq Files
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Manipulate Sequences In Fastq Files
Popular Question 14 months ago, created a question with more than 1,000 views. For Two Positions in Bioinformatics Core Facility, Newcastle, UK
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: What Would You Recommend Me For A One Year Project: Develop A Bioinformatics Sof
Appreciated 14 months ago, created a post with more than 5 votes. For A: Manipulate Sequences In Fastq Files
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Does Bowtie2 Map Multiple Reads To The Same Gene?
Pundit 23 months ago, created a comment with more than 10 votes. For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Popular Question 23 months ago, created a question with more than 1,000 views. For Two Positions in Bioinformatics Core Facility, Newcastle, UK
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Manipulate Sequences In Fastq Files
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Manipulate Sequences In Fastq Files
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Parsing Pdbcodes To Their Cath Numbers
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How Would You Define If A Peptide Is Exposed At The Surface Of A Protein?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For What License Do You Use When You Release Code And Data?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Manipulate Sequences In Fastq Files
Appreciated 4.0 years ago, created a post with more than 5 votes. For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Parsing Pdbcodes To Their Cath Numbers
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Should We Accept The Terms For The Migration To Stackexchange 2.0
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Bioinformatics Career Survey 2011/2012
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Where Can I Get Stats For Previous Uniprot Release?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: What Is The Most Appropriate Uri For A Journal Article?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Your Favorite Bioinformatics Blogs (October 2011)
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Color Pdb According To Amino-Acid Conservation

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