ISMB 2018: BioinfoCoreWorkshop - Revision history

Alastair.kerr at 08:26, 17 September 2018

2018-09-17T08:26:25Z

Mcm: /* Part D: Small group discussion */

2018-07-12T15:59:38Z

Part D: Small group discussion

Mcm: /* Part D: Small group discussion */

2018-07-11T03:17:25Z

Part D: Small group discussion

Mcm: /* Part D: Small group discussion */

2018-07-11T03:04:26Z

Part D: Small group discussion

Mcm: /* Workshop Overview */

2018-06-22T17:52:46Z

Workshop Overview

Mcm: /* Workshop Overview */

2018-06-22T16:18:23Z

Workshop Overview

Bgrichter: /* Workshop Overview */

2018-05-09T15:40:28Z

Workshop Overview

Mcm: /* Presentation Overview */

2018-04-25T15:58:18Z

Presentation Overview

Mcm at 15:57, 25 April 2018

2018-04-25T15:57:05Z

Mcm at 15:56, 25 April 2018

2018-04-25T15:56:40Z

@@ Line 107: / Line 107: @@
 "Lock them in a room" with a competancy test, something they would have to do on the job. Give them 40 minutes for a task that might take 25 minutes. Examples were fixing a broken script (multiple languages available) or writing an email (maybe that's for a different type of job, but something like that). Would you want to go on a camping trip with them? Coffee or lunch with the group can be a good enticement, give them a feel for the group, give you a feel for how they interact. Send ahead of time an RNA-seq analysis and have them run it, present results at the interview. Most people hadn't had any formal recruitment training. Entry level hiring is easier, but they may only stay 2-3 years. Is there a track to PI level, some people have that. Recruits should have a presence in github. Have them provide examples of how they solved a problem and search for evidence of their autonomy and ability to teach themselves new things. Hiring is part vetting and part seduction. How do you make the job attractive, sell it. Work for the common good? Crosstraining available within group. Put a link to your group website in job description, and then ask in the interview if they've been to your website. Bad sign if they haven't.
-Workflow small group (my notes are sketchy, please add)
-CWL/WDL. Airflow. Docker. GA4GH. Why did I write all this, I don't know... :) This group is interested in a communication mechanism, maybe a slack channel or maybe a part of biostars?
+'''Workflow small group '''
 Experimental failures small group:
@@ Line 126: / Line 157: @@
 We will try to get the details on who checks the bioinfo-core box when registering... Right now (supposedly) ISCB will add those people to our mailing list, but we have not confirmed that this is happening. It would be good to verify.

@@ Line 45: / Line 45: @@
 |-
 |2:16 PM - 2:24 PM
-|nf-core: community-driven best-practice Nextflow pipelines
+|nf-core: community-driven best-practice Nextflow pipelines ([https://slides.com/apeltzer/ismb2018-nfcore#/ slides])
 |Alexander Peltzer, Quantitative Biology Center, Tübingen, Germany
 |-
 |2:24 PM - 2:32 PM
-|Data Science in the 21st Century: Streaming Public Data into Containerized Workflows
+|Data Science in the 21st Century: Streaming Public Data into Containerized Workflows ([http://bioinfo-core.org/index.php/File:Containers_Workflows_Lightning_v2.pptx slides])
 |Ben Busby, NCBI, United States
 |-
 |2:32 PM - 2:40 PM
-|Shesmu - An analysis orchestration system designed for FAIR standards and the GA4GH cloud ecosystem
+|Shesmu - An analysis orchestration system designed for FAIR standards and the GA4GH cloud ecosystem ([http://bioinfo-core.org/index.php/File:ljorgensen_ISMB_2018_biocore.pptx slides])
 |Lars Jorgensen, OICR, Canada
 |-
 |2:40 PM - 2:48 PM
-|A (Fire)Cloud-Based DNA Methylation Data Preprocessing and Quality Control Platform
+|A (Fire)Cloud-Based DNA Methylation Data Preprocessing and Quality Control Platform ([http://bioinfo-core.org/index.php/File:ISMB_LighteningTalk.pptx slides])
 |Divy Kangeyan, Harvard University, United States
 |-
 |2:48 PM - 2:56 PM
-|Usability of Marginal Data
+|Usability of Marginal Data ([http://bioinfo-core.org/index.php/File:Thimmapuram_ISMB2018.pptx slides])
 |Jyothi Thimmapuram, Purdue University, United States
 |-
 |2:56 PM - 3:04 PM
-|Experimental Failures
+|Experimental Failures ([http://bioinfo-core.org/index.php/File:Termination_of_Bad_Projects_-_Experimental_Failures1.pdf slides])
 |Krishna Karuturi, The Jackson Laboratory, United States
 |-
@@ Line 113: / Line 113: @@
 Have evidence before pointing fingers... Some groups go-pro film a sample prep, can you imagine. Jointly meet with PIs. Force people to fill out metadata spreadsheet or form before project? Earlier involvement of analysts is better. Some places have a conflict resolution mechanism btw groups.
-Ideas for follow up
+Ideas for group operations to follow up on:
 Cloud again?
-More time? 3 hours next time?
+Cloud/workflow discussion again?
--5 small groups might be better?
-Do we need to alter our communication strategy? Slack was mentioned. ISCB may give us access to Zoom for conf calls.
+More time? Ask for 3 hours next time. One comment that 8 minutes is too short, but some people liked it.
-We could have bionfo-core posters, one would get a $ prize, plus it would be informative and a way to figure out which talks to have...
-We could try to get sponsors, funds would be held in escrow w/ iscb, could pay for travel fellowships for speakers / poster presenters.
+-5 small groups might be better.
 We will try to get the details on who checks the bioinfo-core box when registering...

@@ Line 37: / Line 37: @@
 |-
 |2:00 PM - 2:08 PM
-|Bioinformatics Core Staffing
+|Bioinformatics Core Staffing ([http://bioinfo-core.org/index.php/File:ISMB_Grimm.pptx slides])
 |Sara Grimm, NIEHS, United States
 |-

← Older revision		Revision as of 03:04, 11 July 2018
Line 76:		Line 76:
	\|		\|
	\|}		\|}
		+
		+
		+	Notes (feel free to contribute or modify)
		+
		+	Sara Grimm: Bioinformatics Core Staffing
		+	They support 60 labs. Embedded support model, staff is assigned to a particular lab. Mentioned needing soft skills to communicate and manage expe ctations. Hiring is done by a contracting agency, so they have little control, and there is local competition. They get applicants from life sciences or sometimes IT mid-career. They want someone comfortable at the command line with at least one programming language, conversant in basic biology. They include a scientist on the interview panel, and make sure being in a core is a good fit with their career goals.
		+
		+	Brent Richter:
		+	Showed (complex) org chart. Ideally, want someone who will stay for 2 or more years. Recommended keeping the job description pretty fresh and detailed. Google similar positions and see what the descriptions are like. Offer learning opportunities and define responsibilities clearly, don't be overly general. What bigger areas can the position grow into, who will they report to, how will their career goals be supported? This is a good chance to clarify the scope of the position. The first 90 days offer immediate feedback/praise/criticism. Check in 5 min weekly - do they need anything? Yearly review is an opportunity to re-recruit high performers, or provide constructive criticism if someone is struggling.
		+
		+	Alex Peltzer: NF-core
		+	Diverse, big, erroneous data. Large scale projects that integrate old with new data. Nextflow allows fast prototyping, task composition, parallelization, containerization. http://nf-co.re to collect pipelines (nextflow, MIT license, docker bundled). Continuous integration testing, stable release tags. Cookie cutter skeleton available for new pipelines, gitter channel.
		+
		+	Ben Busby:
		+	WE CAN SAVE COMPBIO by submitting data FOR biologists. Lots of free cloud out there, just call it 'education'. Docker vs Singularity - Singularity offers user same permissions (doesn't req root) may be more comfortable for IT. Antibiotic resistance pipeline, simple enough for juniors in college. Prokaryotic genome pipeline. Nanopore simple enough for high schoolers. ATACflow, Jupyter notebook "press the triangles". Mentioned Google collaboratory.
		+
		+	Lars Jorgensen:
		+	Shesmu. They get the samples nobody else wants to sequence. No "standard" pipeline. Niassa (seqware fork). "Deciders", but infrastructure is troublesome. hard to write and debug, large memory reqs. Shesmu - decider server. Olives - determine what actions to do. Stateless, so recovers nicely if server dies. Olives make jira tickets if something is missing. Good: unified interface. Bad: They are now maintaining a compiler. oicr-gsi/shesmu.
		+
		+	Divy Kangayan
		+	Firecloud - scalable genomic analysis. Need something scalable, reproducible, access to public data, best practices. Mainly applied to methylation data so far. R and scmeth, WDL glues tools together. Lots of QC, read cvg, cpg cvg, cpg density, m bias plot.
		+
		+	Jyothi Thimmapurum
		+	Data that is close to the lower limit of qualification, barely exceeding the minimum requirements. How do you use it? Why did it fail? Experimental design failures - insufficient replicates, wrong type of reads, too few reads. Contamination - sample mix ups, contamination during sample processing or lib prep. Mistakes in protocol, or seq machine failures. Plant DNA can confound studies of bacterial endophytes. WT/mut experiment, but SNPs same in ALL samples, hmmm. Repurpose the data if possible. Still might be able to address some questions or give them some useful info. Txome assembly instead of RNA-seq. You can still learn SOMEthing. Also can be data analysis failures - often fixable - wrong ref genome, wrong analysis methods, how you dealt with missing data. Data interp failures, didn't do multiple hypothesis testing.
		+
		+	Krishna Karuturi
		+	Not really a fun topic, but an important, sticky topic. They have 100 labs. Prevention is better than cure. Exp failures affect relationships with labs and timing. What we really NEED are superheroes, but... They do a multi-point QC inspection. When an experiment fails, do a design re view and figure out why or where they could have caught it. Need to decide if its a drop/no drop situation. In the case of confounding batch effects, if the biological effect being testing is much larger than the batch effect, perhaps proceed with caution. Limit "free" time for projects, or they will lag and drag on.
		+
		+	Hiring/Interviewing small group:
		+	"Lock them in a room" with a competancy test, something they would have to do on the job. Give them 40 minutes for a task that might take 25 minutes. Examples were fixing a broken script (multiple languages available) or writing an email (maybe that's for a different type of job, but something like that). Would you want to go on a camping trip with them? Coffee or lunch with the group can be a good enticement, give them a feel for the group, give you a feel for how they interact. Send ahead of time an RNA-seq analysis and have them run it, present results at the interview. Most people hadn't had any formal recruitment training. Entry level hiring is easier, but they may only stay 2-3 years. Is there a track to PI level, some people have that. Recruits should have a presence in github. Have them provide examples of how they solved a problem and search for evidence of their autonomy and ability to teach themselves new things. Hiring is part vetting and part seduction. How do you make the job attractive, sell it. Work for the common good? Crosstraining available within group. Put a link to your group website in job description, and then ask in the interview if they've been to your website. Bad sign if they haven't.
		+
		+	Workflow small group (my notes are sketchy, please add)
		+	CWL/WDL. Airflow. Docker. GA4GH. Why did I write all this, I don't know... :) This group is interested in a communication mechanism, maybe a slack channel or maybe a part of biostars?
		+
		+	Experimental failures small group:
		+	Have evidence before pointing fingers... Some groups go-pro film a sample prep, can you imagine. Jointly meet with PIs. Force people to fill out metadata spreadsheet or form before project? Earlier involvement of analysts is better. Some places have a conflict resolution mechanism btw groups.
		+
		+	Ideas for follow up
		+	Cloud again?
		+	More time? 3 hours next time?
		+	4-5 small groups might be better?
		+	Do we need to alter our communication strategy? Slack was mentioned. ISCB may give us access to Zoom for conf calls.
		+	We could have bionfo-core posters, one would get a $ prize, plus it would be informative and a way to figure out which talks to have...
		+	We could try to get sponsors, funds would be held in escrow w/ iscb, could pay for travel fellowships for speakers / poster presenters.
		+	We will try to get the details on who checks the bioinfo-core box when registering...

← Older revision		Revision as of 17:52, 22 June 2018
Line 29:		Line 29:
	==Part D: Small group discussion==		==Part D: Small group discussion==
	During this longer session, audience members will divide into groups based on their own interests. Groups will come up with their main take away points and bring them back to the main audience for knowledge sharing and for further discussion. Topics may include all previous presentation areas as well as other areas of interest to running or working within a bioinformatics core facility such as single cell analysis or long read analysis.		During this longer session, audience members will divide into groups based on their own interests. Groups will come up with their main take away points and bring them back to the main audience for knowledge sharing and for further discussion. Topics may include all previous presentation areas as well as other areas of interest to running or working within a bioinformatics core facility such as single cell analysis or long read analysis.
		+
		+	{\|class="wikitable"
		+	\|-
		+	\|Time
		+	\|Title
		+	\|Authors
		+	\|-
		+	\|2:00 PM - 2:08 PM
		+	\|Bioinformatics Core Staffing
		+	\|Sara Grimm, NIEHS, United States
		+	\|-
		+	\|2:08 PM - 2:16 PM
		+	\|Characteristics of a highly successful candidate and how to find them
		+	\|Brent Richter, Partners HealthCare, United States
		+	\|-
		+	\|2:16 PM - 2:24 PM
		+	\|nf-core: community-driven best-practice Nextflow pipelines
		+	\|Alexander Peltzer, Quantitative Biology Center, Tübingen, Germany
		+	\|-
		+	\|2:24 PM - 2:32 PM
		+	\|Data Science in the 21st Century: Streaming Public Data into Containerized Workflows
		+	\|Ben Busby, NCBI, United States
		+	\|-
		+	\|2:32 PM - 2:40 PM
		+	\|Shesmu - An analysis orchestration system designed for FAIR standards and the GA4GH cloud ecosystem
		+	\|Lars Jorgensen, OICR, Canada
		+	\|-
		+	\|2:40 PM - 2:48 PM
		+	\|A (Fire)Cloud-Based DNA Methylation Data Preprocessing and Quality Control Platform
		+	\|Divy Kangeyan, Harvard University, United States
		+	\|-
		+	\|2:48 PM - 2:56 PM
		+	\|Usability of Marginal Data
		+	\|Jyothi Thimmapuram, Purdue University, United States
		+	\|-
		+	\|2:56 PM - 3:04 PM
		+	\|Experimental Failures
		+	\|Krishna Karuturi, The Jackson Laboratory, United States
		+	\|-
		+	\|3:04 PM - 3:20 PM
		+	\|Small Group Discussions
		+	\|
		+	\|-
		+	\|3:20 PM - 4:00 PM
		+	\|Report to all present the insights obtained within the small group discussions
		+	\|
		+	\|}

@@ Line 3: / Line 3: @@
 =Workshop Overview=
-The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm.
+The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm in Columbus EF at the Hyatt Regency in Chicago.
-The workshop will explore three topics relevant to bioinformatics core facilities. Members of core facilities will share their experience and insights in lightning talks to introduce the topics and some of the issues followed by topical small group discussions to deepen and expand upon the topics.
+The bioinformatics core workshop is a workshop by practitioners and managers of Core Facilities for all members of core facilities, including scientists, engineers, analysts, operations and management staff. In this 15th year of bringing the Core community together at ISMB, we will explore in-depth three topics relevant to bioinformatics core facilities through lightning talks that broadly explore each area followed by small-group break out discussions with insights brought back to the full audience for further discussion and knowledge share.
 Organizers:
@@ Line 16: / Line 16: @@
 ==Part A: Strategies for Hiring, Recruiting, and Interviewing new bioinformaticians==
-* finding and hiring people
-* interview techniques and questions
+Methods to find, interview and hire highly successful staff and bioinformaticians for a core facility. Speakers will introduce experience and challenges including finding and hiring people, interview techniques and questions and best practices for recruiting candidates
 ==Part B: Containerization, Clouds, and Workflows==
-* cloud infrastructure limitations and recommendations
-* Key datasets in Clouds
+Topics to be covered include cloud infrastructure recommendations and limitations, key datasets of value hosted in the cloud, containerization technology that works and workflow tool development and results.
 ==Part C: When good experiments go bad: Negotiating experiment quality failures==
-* detecting failure
-* guidelines for terminating bad projects
+A non-exhaustive survey of methods and successes in detecting failures and exploring guidelines for terminating bad projects.
 ==Part D: Small group discussion==
-During this session, audience members will divide into groups based on their own interests. Groups will discuss the areas introduced (or other issues, concerns and ideas), then come up with their main take away points and bring them back to share with the larger group. Topics may include:
+During this longer session, audience members will divide into groups based on their own interests. Groups will come up with their main take away points and bring them back to the main audience for knowledge sharing and for further discussion. Topics may include all previous presentation areas as well as other areas of interest to running or working within a bioinformatics core facility such as single cell analysis or long read analysis.

@@ Line 5: / Line 5: @@
 The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm.
-The workshop will explore three topics relevant to bioinformatics core facilities. Members of core facilities will share their experience and insights in lightning talks followed by topical small group discussions.
+The workshop will explore three topics relevant to bioinformatics core facilities. Members of core facilities will share their experience and insights in lightning talks to introduce the topics and some of the issues followed by topical small group discussions to deepen and expand upon the topics.
 Organizers:
@@ Line 31: / Line 31: @@
 ==Part D: Small group discussion==
-During this session, audience members will divide into groups based on their own interests. Groups will come up with their main take away points and bring them back to the larger group. Topics may include:
+During this session, audience members will divide into groups based on their own interests. Groups will discuss the areas introduced (or other issues, concerns and ideas), then come up with their main take away points and bring them back to share with the larger group. Topics may include:
 * interviewing / hiring / etc.
 * containers, clouds, workflows

← Older revision		Revision as of 15:58, 25 April 2018
Line 1:		Line 1:


−	=~~Presentation~~ Overview=	+	=Workshop Overview=

	The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm.		The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm.

@@ Line 1: / Line 1: @@
 Organizers:
@@ Line 6: / Line 14: @@
 * Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
 * Alberto Riva, University of Florida, United States
 ==Part A: Strategies for Hiring, Recruiting, and Interviewing new bioinformaticians==

@@ Line 1: / Line 1: @@
 Organizers:
-Madelaine Gogol, Stowers Institute, United States
+* Madelaine Gogol, Stowers Institute, United States
-Hemant Kelkar, University of North Carolina, United States
+* Hemant Kelkar, University of North Carolina, United States
-Alastair Kerr, University of Edinburgh, United Kingdom
+* Alastair Kerr, University of Edinburgh, United Kingdom
-Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
+* Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
-Alberto Riva, University of Florida, United States
+* Alberto Riva, University of Florida, United States
 =Presentation Overview=