Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 9: Line 9:
 
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
= 2014 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2014|January]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2014|February]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
== February 6, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
=== AGENDA ===
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
* Topic Curation
 
** WS243,244: Innate immunity and response to pathogens
 
** WS242: miRNA pathway
 
** WS241: UPR pathways
 
** using the caltech FTP site for storing topic page pathway images for the web team. Where is it, what information do we want to include, can we use this to track history of pathways?
 
** model change to put topics in hierarchical structure.
 
* File cabinets in hallway?
 
* Variations that have lost a public_name due to Million Mutation processing in WS240.
 
** What to do with ones that have phenotypes attached, should they have their public_names restored, so we can see them in our OA dropdown lists?
 
<pre>
 
> WBVar00249046 former public-name sy5417
 
> WBVar00275318 former public-name y87
 
> WBVar00275321 former public_name y95
 
> WBVar00000714 former public_names cb107, cbs107
 
> WBVar00000718 former public_names cb111, cbs111
 
> WBVar00000716 former public_names cb109, cbs109
 
> WBVar00000720 former public_names cb113, cbs113
 
> e2518 is an other_name of WBVar0014462
 
> g320 is an other_name of WBVar00017601
 
</pre>
 
* Models meeting in Toronto March 10-11
 
  
=== Gene Association files ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
* Life stage-gene associations
 
* Capturing relations (e.g. "involved_in") in GAF; how to do that for life stage?
 
* What search tool do we plan for e.g. "what genes are expressed in a particular neuron AND during dauer larval stage?"
 
  
we can use WormMine. Example query:
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
http://www.wormbase.org/tools/wormmine/template.do?name=Anatomy_LS_Genes&scope=all
 
  
* Expression data model needs updating to capture BOTH place AND time of gene expression
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
=== Pathway images on topic pages ===
 
* Do we store/supply a flat image file for the web team?
 
* Store image files on the FTP site? Canopus, nightly mirroring
 
* Release-specific directories/images? OICR needs to know and handle
 
* Daniela's images are collected cumulatively; Wen's are overwritten
 
* May be an issue embedding iFrame interactive viewer
 
  
=== Variations losing public names ===
+
==March 14, 2024==
* Million Mutation project, variations getting renamed
 
* Distinguishing natural variants vs. lab-induced alleles
 
* Merging event (natural variants at same location merged), existing names become "Other_name"s
 
* Can we have a mechanism in place to decide one Public_name if there are multiple? Temporal precedence?
 
* First published name can be official Public_name?
 
* decided to leave things as they are
 
  
 +
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
== February 13, 2014 ==
+
===NER with LLMs===
  
=== AGENDA ===
+
* Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
* Infection model
 
* Reminder: Alex Pico, Mary Ann Tuli, Xiaodong visiting Caltech Feb 24th
 
* Sequence Feature interactors
 
* Viewing list of topics in OA
 
  
=== Infection model ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
*Infection model discussion--Advantages/disadvantages to curating to the level of strain for pathogens like Bacteria, Fungi etc) (Ranjana)
 
Please see http://wiki.wormbase.org/index.php/Modeling_data_for_Infectious_agents
 
*Do we create non-nematode Strain objects here at Caltech? (Ranjana)
 
** (Mary Ann) As far as I can see, no. But I don't see a reason why you can't if there is a need. We will simply need to make sure you know the right curation format, which for non-nematode strains is a bit vague. I am talking to Aric shortly about the  Db11 strain you sent me earlier this week.
 
*Things to consider:
 
** Creation of "?Infection" class
 
** Species-species interactions versus more specific strain-strain interactions
 
** Should we create topics that represent species-species interactions that can then be associated to relevant strain-strain interaction objects of an "?Infection" class?
 
* We would like to be able to create/manage new strains, nematode and non-nematode, for these annotations
 
* Strain OA?
 
  
=== WikiPathways meeting ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Feb 24th with Alex Pico
 
* Comments and requests for WikiPathways can be posted on [http://wiki.wormbase.org/index.php/WikiPathways_Questions_%26_Comments Wiki page]
 
* Alex Pico will present updates to viewer/editor (new JS viewer/editor)
 
  
=== Topic list in OA ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Xiaodong requesting Topic list viewer
 
* Best to just have a browser window/tab open with topics listed, either in Process Term OA or in the Curation Status form
 
  
=== Feature interactors ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Some interaction objects currently refer to multiple sequence feature objects in addition to a regulator gene and a regulated gene; this results in "hairballs" in interactions, Cytoscape view
 
* We probably want a separate widget/viewer for gene/protein-sequence feature interactions involving a GBrowse window, displaying the interacting sequence feature in the context of the genome (to infer relevant genes, for example)
 
* Need to consider options for display and annotation (e.g. should we only have binary interactions?)
 
  
== February 20, 2014 ==
 
  
=== AGENDA ===
 
* Pathways in general and WikiPathways<br>
 
To plan for Alex's visit, it would be good to solidify our wants and needs for process and pathway visualization. Please add specific questions for Alex to the [[WikiPathways_Questions_%26_Comments]] page. <br>
 
Some global discussion points for our in-house Caltech meeting:
 
** what do we want our pathways to show?
 
** how do we want pathways displayed?
 
* Schedule your meeting with Mary Ann and or Alex. Either add yourself to the Calendar or let Karen know when you have time to chat.
 
  
=== Alex Pico's visit for WikiPathways ===
+
==February 15, 2024==
* WormBase calendar; add in when you want to speak to Alex
 
* Alex will present, have general discussion in Kerckhoff 024 at 10am on Monday
 
* Chris, Karen, et al meet with Alex
 
* Alex leaving at 2:30pm
 
* Web meeting 1:30pm (Google Hangout); Alex talk to web team to integrate WikiPathway images, etc.
 
* Integrating WormBase data to automatically inform construction of pathways?
 
* We can try to setup a live stream (Google Hangout?) of Alex's talk for Kimberly and Daniela
 
  
=== Mary Ann's visit ===
+
=== Literature Migration to the Alliance ABC ===
* Meet with Paul at 9am
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Alex Pico's talk at 10am
+
===== Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic =====
* 10:45am - 12pm, Mary Ann can circulate around curators
+
*Facet for topic
* Lunch
+
*Facet for automatic assertion
* Chris and Karen can meet after 2:30pm or Tuesday
+
**neural network method
* Tuesday morning Skype with Kimberly
+
*Facet for confidence level
* Daniela can talk with Mary Ann on Europe time
+
**High
* Arrive ~2pm tomorrow (Friday 21st)
+
*Facet for manual assertion
* Dinner 21st, 22nd, 23rd?
+
**author assertion
* ?Construct model intro discussion Monday afternoon?
+
***ACKnowledge method
* Tuesday morning ?Construct model call (w/Daniela)
+
**professional biocurator assertion
 +
***curation tools method - NULL
  
=== LEGO tool prototype ===
+
===== Manually validate paper - topic flags without curating =====
* Paul Thomas made a new LEGO prototype tool
+
*Facet for topic
* Allows visual GUI-based LEGO annotations
+
*Facet for manual assertion
* Example link: http://go-genkisugi.rhcloud.com/seed/model/gomodel:wb-GO_0043053
+
**professional biocurator assertion
* Base link: http://go-genkisugi.rhcloud.com/
+
***ABC - no data
* See also:  [[File:PThomaslego-Whitepaper-2010-03.pdf]]
 
  
=== Paul met with ZFIN ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Interested in human disease relevance & pathways
+
* Search ABC with paper identifier
 +
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
=== Human Disease relevance ===
+
=== PDF Storage ===
* FlyBase should have data out in March
+
* At the Alliance PDFs will be stored in Amazon s3
* Ranjana et al working on paper
+
* We are not planning to formally store back-up copies elsewhere
* OMIM connnections
+
* Is this okay with everyone?
  
=== Odd OA behavior ===
+
==February 8, 2024==
* Karen pointed out (Chris confirms) strange behavior where data persists in fields that should be empty
+
* TAGC
* Browser specific? Occurs on both Firefox and Chrome
+
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
== February 27, 2014 ==
+
==February 1, 2024==
 +
* Paul will ask Natalia to take care of pending reimbursements
 +
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
=== Agenda ===
+
==January 25, 2024==
* Changes to ?Construct and ?Transgene models
 
**see [http://wiki.wormbase.org/index.php/WormBase_Model:Construct Construct model] page
 
**see [http://wiki.wormbase.org/index.php/Talk:WormBase_Model:Construct discussion] of proposed Construct model
 
* Sequence feature (?Feature) curation
 
* Mapping constructs to the genome, when not sequence features, i.e. artificial constructs used for expression. Gary W suggests to capture the info in a DNA_text field as it happens for RNAi. Who should pull up the sequence? Gary says:
 
I would expect that someone at Caltech could write a simple script to
 
pull out this sequence for you, given the input coordinates, a GFF file
 
containing CDS objects and a genome sequence. If not, we could knock one up for you.
 
Example: -4770 to +3592 (relative to the gene translation start)
 
  
* Topic curation
+
=== Curator Info on Curation Forms ===
**Innate immune response and defense response terms in GO (Kimberly)
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
***GO annotations for many of the genes involved in innate immune response have been annotated to both innate immune response and to a defense response term, such as 'defense response to Gram negative bacterium'. However, for a number of C. elegans genes, these two annotations are really referring to the same process.
 
***I'd like to propose new GO terms that have the specificity of the defense response terms wrt the specific type of pathogen, but are child terms of innate immune response.  Then, where appropriate, we'd consolidate our annotations onto one new term, for example, 'innate immune response to Gram negative bacterium'.
 
***Also, I'd like to propose a revision to the current definition of 'innate immune response' in GO:
 
  
  Current definition:  Innate immune responses are defense responses mediated by germline encoded components that directly recognize
+
=== ACKnowledge Author Request - WBPaper00066091 ===
  components of potential pathogens.  
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
  Proposed new definition: A protective response induced in an organism by the presence of a pathogen (e.g., bacterial, viral,
+
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.  
  microsporidial). The innate immune response is mediated by molecules that directly recognize pathogen components and by signaling
 
  pathways that coordinate the subsequent defense response.
 
  
 +
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  
=== ?Construct & ?Transgene ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Engineered alleles need an annotation method
 
** Crispr, Mos Sci, etc.
 
** Inserted transgenes (engineered (e.g. "Si") or integrated ("Is")), modified genes
 
* We need ?Variations and ?Transgenes to have a common link via ?Construct (and identity to one another)
 
* If there are known flanking sequences (unique insertion site in the genome) for any transgene, it will also become an allele (?Variation) object
 
* Mary Ann will create the ?Variation objects for ?Transgenes that meet the criteria
 
* Consequences for ?Expr_pattern
 
** ?Transgenes are used in expression pattern curation
 
** ?Construct can be assigned an ?Expr_pattern
 
** ?Feature objects (sequence features) can be assigned to a ?Construct
 
* ?Feature objects have been sent to Mary Ann and Gary Williams by curators (Xiaodong, Daniela, etc.) to create and approve the ?Features for a paper
 
* We will want a faster, more efficient pipeline for requesting ?Feature objects
 
  
== March 6, 2014 ==
+
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 18:18, 14 March 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings


March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics