ISMB 2017: BioinfoCoreWorkshop - Revision history

Ewels: Tidied links etc for Phil's talk.

2017-07-25T13:08:51Z

Tidied links etc for Phil's talk.

Rshamilton: /* Managing a Core Facility */

2017-07-25T08:52:19Z

Managing a Core Facility

Bgrichter: /* Ensuring Reproducibility */

2017-07-24T12:20:45Z

Ensuring Reproducibility

Bgrichter at 12:19, 24 July 2017

2017-07-24T12:19:47Z

Bgrichter at 12:15, 24 July 2017

2017-07-24T12:15:55Z

Mcm: /* Workshop topics */

2017-07-13T19:19:36Z

Workshop topics

Mcm: /* Workshop topics */

2017-07-13T13:37:45Z

Workshop topics

Mcm: /* Workshop topics */

2017-07-13T13:37:21Z

Workshop topics

Mcm: /* Workshop topics */

2017-07-13T13:36:22Z

Workshop topics

Mcm: /* Workshop topics */

2017-07-13T13:35:14Z

Workshop topics

@@ Line 58: / Line 58: @@
 [[File:Phil_Ewels_ISMB_BioinfoCore_2017.pdf]]
-Core facility for all of Sweden.  Maintain a continuum of QC, from fully automated and rigorous using MultiQC to the occasional QC  for development.  utilizes continuous integration: GitHub, docker and travis CL.   uses [https://github.com/search?q=topic%3Anextflow&type=Repositories Nextflow] for NGI-RNAseq and others.
+Core facility for all of Sweden.  Maintain a continuum of QC, from fully automated and rigorous using MultiQC to the occasional in-depth QC validations. Utilizes continuous integration for analysis pipelines: GitHub, docker and Travis CI. Uses [http://nextflow.io/ Nextflow] for [https://github.com/SciLifeLab/NGI-RNAseq NGI-RNAseq] and others ([https://github.com/SciLifeLab/NGI-ChIPseq NGI-ChIPseq], [https://github.com/SciLifeLab/NGI-MethylSeq NGI-MethylSeq], [https://github.com/SciLifeLab/NGI-smRNAseq NGI-smRNAseq], [https://github.com/SciLifeLab/CAW Cancer Analysis Workflow]). Everything is on GitHub, see http://opensource.scilifelab.se, http://multiqc.info, https://github.com/SciLifeLab.
 '''Reproducible and fully documented data analyses at the Functional Genomics Center Zurich'''<br>
@@ Line 70: / Line 69: @@
 '''Reproducibility Discussion: 12-12:30'''
-Opitz: How do you deal with external clients and data backup?  Data is backed up by policy.  the users signs up for retention of their data for a period of time--industry and external users understand their data is captured and kept for 3-6 months.  QC results are kept forever but original data is purged.
+''Opitz: How do you deal with external clients and data backup?''  Data is backed up by policy.  the users signs up for retention of their data for a period of time--industry and external users understand their data is captured and kept for 3-6 months.  QC results are kept forever but original data is purged.
-What is everyone's definition of reproducibility?  is it that you are able to run the data again in 10 years and get the same results and are you ensured to get the same results?  Ewels has everything on GitHub and can re-run data using  specific version of tools branched on GitHub.
+''What is everyone's definition of reproducibility?''  is it that you are able to run the data again in 10 years and get the same results and are you ensured to get the same results?  Ewels has everything on GitHub and can re-run data using  specific version of tools branched on GitHub.
 [http://singularity.lbl.gov singularity] to run containers on HPC.
 ISO certification: validation steps, everything is audited, complete documentation system around the IT and informatics systems.
-Do you have a sense as to whether your users understand the investments you have done to setup such a rigorous system?  a lot of people couldn't reproduce their old pipeline and didn't trust them. They've written the QC measures to demonstrate quality,
+''Do you have a sense as to whether your users understand the investments you have done to setup such a rigorous system?''  A lot of people couldn't reproduce their old pipeline and didn't trust them. They've written the QC measures to demonstrate quality,
 the value and improve reproducibility and trust.
 try to develop interactive tools with SHINY.

@@ Line 17: / Line 17: @@
 Speaker: '''Russell Hamilton''', University of Cambridge<br>
 Time: 10:00-10:15<br>
@@ Line 47: / Line 49: @@
 Different organizational structures: study/survey opportunity--reporting to an academic?  working inside institutional funding?
 ===Ensuring Reproducibility===

← Older revision		Revision as of 12:20, 24 July 2017
Line 65:		Line 65:

	Leverages an Open Technology Platform since 2002		Leverages an Open Technology Platform since 2002
		+

	'''Reproducibility Discussion: 12-12:30'''		'''Reproducibility Discussion: 12-12:30'''

@@ Line 11: / Line 11: @@
 == Workshop topics ==
-'''Managing a Core Facility'''
+===Managing a Core Facility===
@@ Line 31: / Line 31: @@
 Some Questions:
 What's your biggest horror story?
-what where some of the traits you look for in a candidate.
+what where some of the traits and abilities you look for in a candidate?
 what's the size of your team(s) and the reporting structure?
-Management Panel: 10:30-11:10
+'''Management Discussion: 10:30-11:10'''
 balance of operating a core and research: research is secondary, but how are you judged?  how do you manage  phd students through the core?  they are co-supervised.
@@ Line 48: / Line 48: @@
 Different organizational structures: study/survey opportunity--reporting to an academic?  working inside institutional funding?
-'''Ensuring Reproducibility'''
@@ Line 65: / Line 66: @@
 Leverages an Open Technology Platform since 2002
-Reproducibility Panel: 12-12:30
+'''Reproducibility Discussion: 12-12:30'''
 Opitz: How do you deal with external clients and data backup?  Data is backed up by policy.  the users signs up for retention of their data for a period of time--industry and external users understand their data is captured and kept for 3-6 months.  QC results are kept forever but original data is purged.
@@ Line 79: / Line 80: @@
 right next store.
 idea of an interactive tool that exports a reproducible script.

@@ Line 1: / Line 1: @@
-We are holding a Bioinfo-core workshop at the [https://www.iscb.org/ismbeccb2017 ISMB/ECCB meeting] in Prague.  We have been given a [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/workshops.php#WK02 half-day slot in the program] on Monday, July 24, 2017, 10:00 am – 12:30 pm
+We are holding a Bioinfo-core workshop at the [https://www.iscb.org/ismbeccb2017 ISMB/ECCB meeting] in Prague.  We have been provided a [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/workshops.php#WK02 half-day slot in the program] on Monday, July 24, 2017, 10:00 am – 12:30 pm
 == Workshop Structure ==
@@ Line 5: / Line 7: @@
 The workshop is split into two sessions with a required break between.  Each session will have two 15 minute talks followed by a 30 minute discussion.
-* The first slot will have 2 15 minute talks on the topic of Managing Core Facilities followed by a 30 minute panel discussion. After the break we will have 2 15 minute talks about Ensuring Scientific Reproducibility, followed by a 30 minute panel discussion.
+* The first slot will have 2 15 minute talks on the topic of Managing Core Facilities followed by a 40 minute audiance discussion. After the break we will have 2 15 minute talks about Ensuring Scientific Reproducibility, followed by a 40 minute panel discussion.
 == Workshop topics ==
@@ Line 15: / Line 17: @@
 Speaker: '''Russell Hamilton''', University of Cambridge<br>
 Time: 10:00-10:15<br>
 '''Managing people in a core facility'''<br>
@@ Line 20: / Line 23: @@
 Time: 10:15-10:30
 '''Ensuring Reproducibility'''

@@ Line 11: / Line 11: @@
 '''Managing a Core Facility'''
-Speaker: Annette McGrath, CSIRO The University of Queensland
+'''Setting up a new bioinformatics core facility: a first year review'''<br>
 Time: 10:15-10:30
 Management Panel: 10:30-11:00
@@ Line 25: / Line 25: @@
 '''Ensuring Reproducibility'''
 [[File:Phil_Ewels_ISMB_BioinfoCore_2017.pdf]]
+'''Reproducible and fully documented data analyses at the Functional Genomics Center Zurich'''<br>
-Speaker: Lennart Opitz, University of Zurich
+Speaker: '''Lennart Opitz''', University of Zurich<br>
-Time: 11:45-12
+Time: 11:45-12<br>
 Reproducibility Panel: 12-12:30

← Older revision		Revision as of 13:37, 13 July 2017
Line 29:		Line 29:

	[[File:Phil_Ewels_ISMB_BioinfoCore_2017.pdf]]		[[File:Phil_Ewels_ISMB_BioinfoCore_2017.pdf]]
		+

	Speaker: Lennart Opitz, University of Zurich		Speaker: Lennart Opitz, University of Zurich

@@ Line 27: / Line 27: @@
 Time: 11:30-11:45
 Title: Developing Reliable QC at the Swedish National Genomics Infrastructure
 [[File:Phil_Ewels_ISMB_BioinfoCore_2017.pdf]]

← Older revision		Revision as of 13:35, 13 July 2017
Line 20:		Line 20:

	Management Panel: 10:30-11:00		Management Panel: 10:30-11:00
		+

	'''Ensuring Reproducibility'''		'''Ensuring Reproducibility'''