ISMB 2019: BioinfoCoreWorkshop - Revision history

Mcm: /* Schedule */

2019-07-26T06:03:36Z

Schedule

Mcm: /* Schedule */

2019-07-26T06:03:04Z

Schedule

Mcm: /* Schedule */

2019-07-26T06:01:54Z

Schedule

Alastair.kerr at 15:59, 24 July 2019

2019-07-24T15:59:56Z

Bgrichter: /* 175 total people over the 2.5 hours (over capacity within room). 55 people participated for the full 2.5 hours including participation in the breakout sessions and discussions. 75 people for final NextFlow Demo */

2019-07-23T12:20:58Z

175 total people over the 2.5 hours (over capacity within room). 55 people participated for the full 2.5 hours including participation in the breakout sessions and discussions. 75 people for final NextFlow Demo

Mcm: /* Workshop Overview */

2019-07-22T13:03:13Z

Workshop Overview

Bgrichter at 10:47, 22 July 2019

2019-07-22T10:47:13Z

Bgrichter: /* Breakout sessions */

2019-07-22T10:20:44Z

Breakout sessions

Bgrichter at 10:18, 22 July 2019

2019-07-22T10:18:56Z

Bgrichter at 10:18, 22 July 2019

2019-07-22T10:18:27Z

@@ Line 78: / Line 78: @@
 |-
 |11:10 - 11:20 AM
-|Development of bioinformatics workshop by a core facility ([Riva-ISMB19-slides-final.pdf slides])
+|Development of bioinformatics workshop by a core facility ([http://bioinfo-core.org/index.php/File:Riva-ISMB19-slides-final.pdf slides])
 |Alberto Riva, University of Florida, United States
 |-

@@ Line 66: / Line 66: @@
 |-
 |10:40 - 10:50 AM
-|Conda and Bioconda, the best thing since sliced bread ([Conda and Bioconda The best thing since sliced bread.pdf slides])
+|Conda and Bioconda, the best thing since sliced bread ([http://bioinfo-core.org/index.php/File:Conda_and_Bioconda_The_best_thing_since_sliced_bread.pdf slides])
 |Devon Ryan, Max Planck Institute, Germany
 |-
@@ Line 74: / Line 74: @@
 |-
 |11:00 - 11:10 AM
-|Bioinformatics training (in the context of a core) ([Bioinfo-core training.pdf])
+|Bioinformatics training (in the context of a core) ([http://bioinfo-core.org/index.php/File:Bioinfo-core_training.pdf slides])
 |Radhika Khetani, Harvard School of Public Health, United States
 |-
 |11:10 - 11:20 AM
-|Development of bioinformatics workshop by a core facility ([Riva-ISMB19-slides-final.pdf])
+|Development of bioinformatics workshop by a core facility ([Riva-ISMB19-slides-final.pdf slides])
 |Alberto Riva, University of Florida, United States
 |-

@@ Line 58: / Line 58: @@
 |-
 |10:20 - 10:30 AM
-|Transitioning bioinformatics core to support biomedical AI/ML research - lessons learned
+|Transitioning bioinformatics core to support biomedical AI/ML research - lessons learned ([http://bioinfo-core.org/images/8/8a/FannBioinfo-Core.pdf slides])
 |Yang Fann, NIH, United States
 |-
 |10:30 - 10:40 AM
-|Supporting single cell RNA-seq analysis: A Core's Perspective
+|Supporting single cell RNA-seq analysis: A Core's Perspective ([http://bioinfo-core.org/index.php/File:Bioinfo-core_singlecell.pdf slides])
 |Shannan Ho Sui, Harvard School of Public Health, United States
 |-
 |10:40 - 10:50 AM
-|Conda and Bioconda, the best thing since sliced bread
+|Conda and Bioconda, the best thing since sliced bread ([Conda and Bioconda The best thing since sliced bread.pdf slides])
 |Devon Ryan, Max Planck Institute, Germany
 |-
 |10:50 - 11:00 AM
-|Improving project management and tracking with Asana and Toggl
+|Improving project management and tracking with Asana and Toggl ([http://bioinfo-core.org/index.php/File:SBR_bioinfo_core_190717.pdf slides])
 |Sara Brin Rosenthal, UCSD, United States
 |-
 |11:00 - 11:10 AM
-|Bioinformatics training (in the context of a core)
+|Bioinformatics training (in the context of a core) ([Bioinfo-core training.pdf])
 |Radhika Khetani, Harvard School of Public Health, United States
 |-
 |11:10 - 11:20 AM
-|Development of bioinformatics workshop by a core facility
+|Development of bioinformatics workshop by a core facility ([Riva-ISMB19-slides-final.pdf])
 |Alberto Riva, University of Florida, United States
 |-
@@ Line 94: / Line 94: @@
 |-
 |}
 == Workshop Discussion ==

← Older revision		Revision as of 15:59, 24 July 2019
Line 1:		Line 1:
		+	= Dinner information =
		+
		+	We will be leaving at 7.30 Wednesday from the reception hall (near the ribbon stand) or see you at the restaurant
		+
		+	Details:
		+	Veranda Pellicanò
		+	Birskopfweglein 7, 4052 Basel, Switzerland
		+	+41 61 311 55 01
		+
		+	https://maps.app.goo.gl/gwWciAvukf7ARhgo9
		+
		+
	=Workshop Overview=		=Workshop Overview=

@@ Line 90: / Line 90: @@
 **Large, diverse datasets from multiple sources both private and public from around the world.
 *Supporting single cell RNA-seq analysis: A Core's Perspective
-**Single cell growing in demand over the last 5 years.  Data analysis is becoming the bottleneck.  Taking a community based approach by collaborating with other HSPS teams and other schools (HMS) to tackle the problem: sequencing core (de-multiplexing), labs (iterative requires research input--is cell cycling part or mitochondria?), training, etc.
+**Single cell growing in demand over the last 5 years.  Data analysis is becoming the bottleneck.  Taking a community based approach by collaborating with other HSPS teams and other schools (HMS) to tackle the problem: sequencing core (de-multiplexing), labs (iterative; requires research input--is cell cycling part or mitochondria?), training, etc.
 **built out bcbio python toolkit with 62 international contributors.
 **settled on serat suite of tools but also uses many others such as multicca
 *Conda and Bioconda, the best thing since sliced bread
-**Installing Software--get asked for help to install, particularly ones that need dependencies.
+**Installing Software--get asked for help to install all kinds of software, particularly ones that carry many dependencies.
-**no route needed, ever.  dependencies are handled for you.
+**with Conda, root access not needed, ever.  dependencies are handled for you.
-**free and can add your own .
+**free and can add your own packages
-**module load activates a condo environment behind the scene
+**module load activates a conda environment behind the scene for them
-**bioconductor packages in bioconda. for every package made a singularity and docker container compiled as well. Biocontainer
+**bioconductor packages in bioconda. for every package they also compile a singularity and docker container. Biocontainer
 **CoreOS--Quay.
-**1700 packages via can over a week.  behind the scene bioconductor upgrading
+**1700 packages upgraded over a week.  behind the scenes, bioconductor upgrading
-**bioconda has 700+ contributors  release your tools.
+**bioconda has 700+ contributors:  release your tools using bioconda.
 *Improving project management and tracking with Asana and Toggl
 **Fee for Service Center with up to 324 projects over the last 4 years.
-**Tracking projects in the transition from 1 team member to another as the project cycles through the experts
+**Need to Track projects intra-team: transition them 1 team member to another as the project cycles through the experts
 **Analysis can be punctuated with long periods of time while investigator writes papers and grants.  Needs to pick up history sometimes a year later.
 **Asana: have defined a workflow within Asana that includes intake, waiting periods, in progress systems, close out and bill

@@ Line 12: / Line 12: @@
 * Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
 * Alberto Riva, University of Florida, United States
 ==Part A: Technologies and Analytical Methods==

@@ Line 77: / Line 77: @@
 == Workshop Discussion ==
 *Transitioning bioinformatics core to support biomedical AI/ML research - lessons learned
@@ Line 131: / Line 132: @@
 **fees help manage demand and help finance pipeline development
 *Conda/bioconda reproducibility

@@ Line 128: / Line 128: @@
 **Asana, trello, Jira
 **time tracking with Toggle and Harvast (app on phone, laptop, etc)
-**Wants: Congluence?
+**Wants: Confluence to integrate project management together with documentation?
 **fees help manage demand and help finance pipeline development
 *Conda/bioconda reproducibility

@@ Line 113: / Line 113: @@
 **successful: filled 50 spots in just a few days and over ½ attending all lectures.  videorecorded and publicly available.
-==Breakout sessions
+==Breakout sessions==
 *Training
 **chunk out training and repackage and create efficiency

← Older revision		Revision as of 10:18, 22 July 2019
Line 74:		Line 74:
	\|-		\|-
	\|}		\|}
		+
		+
		+	== Workshop Discussion ==
		+
		+	*Transitioning bioinformatics core to support biomedical AI/ML research - lessons learned
		+	**Large, diverse datasets from multiple sources both private and public from around the world.
		+	*Supporting single cell RNA-seq analysis: A Core's Perspective
		+	**Single cell growing in demand over the last 5 years. Data analysis is becoming the bottleneck. Taking a community based approach by collaborating with other HSPS teams and other schools (HMS) to tackle the problem: sequencing core (de-multiplexing), labs (iterative requires research input--is cell cycling part or mitochondria?), training, etc.
		+	**built out bcbio python toolkit with 62 international contributors.
		+	**settled on serat suite of tools but also uses many others such as multicca
		+	*Conda and Bioconda, the best thing since sliced bread
		+	**Installing Software--get asked for help to install, particularly ones that need dependencies.
		+	**no route needed, ever. dependencies are handled for you.
		+	**free and can add your own .
		+	**module load activates a condo environment behind the scene
		+	**bioconductor packages in bioconda. for every package made a singularity and docker container compiled as well. Biocontainer
		+	**CoreOS--Quay.
		+	**1700 packages via can over a week. behind the scene bioconductor upgrading
		+	**bioconda has 700+ contributors release your tools.
		+	*Improving project management and tracking with Asana and Toggl
		+	**Fee for Service Center with up to 324 projects over the last 4 years.
		+	**Tracking projects in the transition from 1 team member to another as the project cycles through the experts
		+	**Analysis can be punctuated with long periods of time while investigator writes papers and grants. Needs to pick up history sometimes a year later.
		+	**Asana: have defined a workflow within Asana that includes intake, waiting periods, in progress systems, close out and bill
		+	**archive data to S3.
		+	**implemented toggl to track time on each project and subtask. Integrates with Asana for project management components.
		+	**allows for obtaining better estimates to people. Have found in general they underestimate work.
		+	*Bioinformatics training (in the context of a core)
		+	**Funders provide FTEs dedicated to training (harvard catalyst, HMS)
		+	**interplay between training and consulting: surge in single cell analysis highlights need for training in this technology
		+	**2/3 time spent on training, the remainder on consulting and understanding best practices
		+	**partner with faculty on teaching for credit--e.g. an R component for their cause
		+	**10:1 student to instructor ratios, 25 per class. Use local resources such as their HPC system. Publish materials on GitHub
		+	*Development of bioinformatics workshop by a core facility
		+	**being asked to provide practical bioinformatics training
		+	**challenges: large and diverse audience which makes it hard to develop a suitable curriculum, limited to 8x1hour courses, need to find source of support
		+	**partnered with the cancer center for admin support, the library for 5-seat lab, faculty for some lectures and research computing for the HiPerGator cluster with a dedicated allocation of cores.
		+	**successful: filled 50 spots in just a few days and over ½ attending all lectures. videorecorded and publicly available.
		+
		+	==Breakout sessions
		+	*Training
		+	**chunk out training and repackage and create efficiency
		+	**signups--under subscription vs. over. Charging to put some skin in the game
		+	**Access to compute.
		+	**Google and AWS use, and cost effective. use of jupyter notebooks are particularly cheap
		+	*Single Cell
		+	**help people help themselves.
		+	**shiny apps
		+	**what let's you know it worked properly? primer dimers, cell ranger but '''serat''' R package is the main thing that came out of it.
		+	**need to talk about the standard set of thresholds
		+	*Project Management
		+	**from Excel to google docs
		+	**Asana, trello, Jira
		+	**time tracking with Toggle and Harvast (app on phone, laptop, etc)
		+	**Wants: Congluence?
		+	**fees help manage demand and help finance pipeline development
		+	*Conda/bioconda reproducibility