Meeting Notes with Helen and Daniel

[loretopaulinojr]

Notes for Each Meetings

[loretopaulinojr]

Meeting November 15, 2023

Things to go over:

• [x] How to Look into Biomass Composition using Memote Results, Completed Steps (Tentative)
• [x] Talk about the UNESCO Ocean Science Conference
• [x] Talk about Bernstein's Paper and how it influenced your project.

[loretopaulinojr]

Meeting November 15, 2023: Biomass Compositions.

If he wants, you can show how one is done with the lipid.

[loretopaulinojr]

Meeting November 15, 2023: UNESCO Conference

Introduction to the 2024 Ocean Decade Conference

Hosted by Spain and co-organized with UNESCO’s Intergovernmental Oceanographic Commission (IOC/UNESCO) in its role as the coordinating agency of the UN Decade of Ocean Science for Sustainable Development, the 2024 UN Ocean Decade Conference will take place on 10-12 April 2024 in the coastal city of Barcelona.

It will be a 3-day, in-person event co-led with a range of partners: Government of Catalonia and the Barcelona City Council through the Barcelona Capital Náutica Foundation, and the Spanish National Ocean Decade Committee, which is led by the Ministry of Science and Innovation through the Spanish Research Council (CSIC).

The conference will be a key moment for governments, leaders, maritime sectors, philanthropy, universities, private sector, NGOs and more, to take stock of the achievements of the first three years of the Ocean Decade and define a collective vision for the coming years. Participants will benefit from concrete examples and best practices in ocean science to deliver “the science we need for the ocean we want”.

A key outcome of the 2024 UN Ocean Decade Conference will be the publication of a set of white papers related to the 10 Decade Challenges, that will identify future priorities for the Ocean Decade to generate the knowledge needed for science-based solutions related to global challenges, such as climate change, food security, biodiversity conservation, sustainable ocean economy, pollution and natural hazards.

Objectives:

i. Showcase and celebrate achievements of the Ocean Decade from 2021 to 2024. ii. Generate consensus on science – policy – society priorities for the Ocean Decade over the next 3 to 5 years through structured dialogue around white papers resulting from the Ocean Decade Vision 2030 Process. iii. Create opportunities for networking to catalyze new partnerships and initiatives amongst diverse stakeholder groups and to bring new partners to the Ocean Decade. iv. Provide a global platform for announcements and commitments to support the solutions-oriented goals of the Ocean Decade. v. Prepare existing and future Ocean Decade partners and initiatives for a visible and meaningful role in the 2025 UN Ocean Conference and related events. vi. Highlight initiatives led by local partners relevant to the Ocean Decade, in particular in relation to activities related to the role of science in the sustainable ocean economy. vii. Raise visibility and awareness of the Ocean Decade and the role of ocean science in sustainable development amongst the general public in Barcelona.

This Guidance Note has been developed to provide information on submissions for presentations that will be made during the Conference.

[loretopaulinojr]

Meeting November 15, 2023: New Project

Bernstein's paper provided a great alternative in looking into how to look at SAR 202. More importantly, deep sea organism and the possible correlation to that of RDOC.

This project has the potential to be the first analysis on SAR 202 using mathematical modeling and a procedure to analyze metabolite that can be link to that of RDOC.

[loretopaulinojr]

Meeting Debrief - [Date]

Thank you for today's meeting! Today, we talked about (I will be doing these debriefings for both our notes! If needed you can always add to what may have been missed.)

Important things: are Bolded and Italicized

1. The steps undergone to gap fill the Azureus Model.

   • Link: Azureus Model Gap Fill
   • It was discussed to automate the process and have concrete steps on how certain biomass components are being made or not.
   • Loreto's notes: it may be best to outline this via a circle map. I think this can be done on a famous website biologist used to make figures.

2. The UNESCO Conference.

   • Conference Link: UNESCO Ocean Decade Conference
   • Due to one of the rubric categories on how a presenter is chosen, ask Vicki if she can look into it. CCOMP can provide funds to travel.
   • Regardless of the outcomes, it is good to have somewhat of an abstract created already to present to any other conferences. Similar to what @Helen recommended, make a presentation of my introduction to this project.
   • Look for other conferences like Gordon Conference ("Friendly Atmosphere").

3. The new direction of the Project.

   • Since the goals of C-Comp do not really dive into RDOC related work, it would be best to do two projects.
     • One that correlates more to the IAMM collection (This looks like it's gearing toward bettering how to analyze these strains on Kbase and other platforms if necessary).
     • Finish the Azureus Model; the next step is looking into how to make the biomass composition more automated.
     • Second, should be more into looking at SAR 202 and, I forgot to mention this, Altermonas Mediterranea which is a species in the IAMM collection is considered a deep-sea species (1000 m depth). I can possibly look into the analysis within a certain water column. I attached a nice paper below that introduced this species. Note: DE1 is the one in the IAMM collection not the type strain DE.
     • The next step is to finish reading the paper and find real ways to do an analysis to see patterns within RDOC research. I can maybe even tie, LDOC.
     • The second step is awaiting access to Matlab through an institution. Vicki is looking into if WHOI has a license or not. If not I will have to wait for my BU email. @dsegre will send an email for needed information to continue the process of getting a BU email.
     • Through MATLAB, replicate David's work with E. coli, then you can move on to your strains.

4. Unrelated Topics I forgot to mention:

   • From November 23, 2023, to November 29, I will be at Virginia to celebrate Thanksgiving.
   • From December 10, 2023, to December 15, I will be at San Diego presenting at AGU.

That should be all from today's meeting! I look forward to using Matlab. Please let me know if you have any questions. Our next meeting will be on November 29, 2023, 2 pm, and it can be on zoom since my flight is at 7 pm.

[loretopaulinojr]

Meeting , January 2024

Things to go over:

• [x] The "To Do" given to the B2P students.
• [x] The Current Project Update
• [x] Extracurricular

[loretopaulinojr]

Meeting , January 2024

Current Project Update.

Steps to Analyze KBase Models with MATLAB

Objective

To replicate the analysis performed in the Bernstein paper using our marine genomes and MATLAB code.

Steps

1. Review the Bernstein Paper

• Study the methodology in the Bernstein paper.
• Understand how they generated KBase models using Python.
• https://github.com/loretopaulinojr/CCOMP/issues/12
• The Url above is the current process on the project.

2. Update the Narrative

• Modify the narrative to integrate the new KBase model building app.
• This has been put on the back burner as of January 16, 2024.
• Suggested to work on the Colab to look into the model.

3. Replace Genomes

• Substitute the genomes mentioned in the paper with our marine genomes.

4. MATLAB Analysis

• Once we obtain the MATLAB code:
  • Use it to perform a detailed analysis with our marine strains.
  • Ensure all functionalities are compatible and functional.

4. MBL

• Vicki does not know the MBL.
• Due date is on February 21, 2024

Questions: The genomes are up in the air

• Helen has the list of genomes, apologize to Konrad.

[loretopaulinojr]

22nd Monday to Wednesday.

Cast 320

[loretopaulinojr]

Meeting Notes

Thank you for today's meeting! Attached below is just little notes after the meeting. Just to continue what was done before.

Important things: are Bolded and Italicized

B2P 2023 Diatom

Following with the group and what was tasked to do.

• Task: Annotate the number in the vantol code.
• The Berstein Paper: Looked into the Kbase Narrative.
• Helen has the IAMM genomes that is in a BU cluster. This cluster can be access through the BU email. Do not manually do it.
• Daniel suggested use two strains to test Daniels Kbase Narrative Code. I will use Azurues and Altermonas Med.
• Priority Step: The next step should just be about the Ecoli model mentioned in the paper. Redo those then the IAMM.

BU Email

After the meeting, I now have access to the BU email verified by IT.

• Email: lpaulino@bu.edu
• ID: U32892051
• Grant access to the learn platform:
  • I have sent Daniel an email for a reminder on granting access to his classes notes.

Conferences

• Abstract should be done by the end of this month.
• Note for Loreto: Use the draft that was based on Bernstein Paper.
• Daniel suggested a collection of conferences and their due date to share with people. Helen seems to be working on this.
• Notes for Loreto: I have the same concept but with REUs, probably best to start one for the conferences.

MBL Courses

From the discussion with Helen and Daniel:

• It seems it is more experimental, but on the website, it talked about "This 4-week experience will give students a deep understanding of the field of symbiosis research through a combination of hands-on research projects, lectures from experts in the field, and interactive workshops."
• From the discussion with MBL communication:
  • Sherr is in charge of the advance courses but was not able to speak today.
  • I've sent an email on my eligibility to apply to this program. I will hold off question until I know where I stand.

Class-related Question

I had a question about the prompt given in class today, but I'll just work on it myself and review the notes in the learn platform.

Journal Club

• Journal Club with the CompB2P at 2 pm this Friday.
• The paper we are discussing: Link to the paper
• Vantoll cited this paper as a guide.
• Helen is willing to join. This is the link that we will be using for the journal club: Zoom Link.
• Notes for Loreto: Give an agenda by tonight for how the journal club should be conducted.

Unrelated Topics I forgot to mention:

• CComp Bermuda Trip is around mid-March.
• I was interviewed by the American Chemical Society for my project at the Arctic. I allowed the direction of the interview to talk about some of the challenges and barriers that Pacific Islanders experience in STEM-related settings. With that said, if the article is published I want to be able to give it traction. Would there be any outlets in BU to speak to about sharing an article to the public?
• In the interview, I also talked about some of the work that I am doing under CCOMP.
• If ever the article gets approved by the final reviewer, I would love to share with you all the article.
• I have communication with the media team in Guam, and if ever this gains traction, I wanted to give physical talks at Guam and other Mariana islands about related concepts in the article in hope of bringing attention to a problem and hopefully inspiring others to work towards the problem.

That should be all from today's meeting!

[loretopaulinojr]

Meeting , February 21 2024

Things to go over:

• [ ] The Abstract
• [ ] The Current Project Update
• [ ] Bermuda Trip around mid March

[loretopaulinojr]

Meeting Notes for February 21, 2024

Thank you for today's meeting! Attached below is just little notes after the meeting. Just to continue what was done before.

Important things: are Bolded and Italicized

Abstract for CIS Conference

It was already turned in.

• Task: Fix some typos and the last sentence.
• If accepted, I plan to talk in at least two high schools about Diversity
• Attend the Student Led Conference and just babble.
• Plan logistics and talk to sister to stay with her.

Current Project Update

The next step was to recreate the figure 2 code:

• Related Pictures:
• It worked, but it was slow and had a warning. Is there way to enhance the process, would using the BU cluster help. Is it normal to see warning reoccurring, ask if they came across a similar problem?
• The PM values are the same which makes me think its not working correctly and that I should read more book on percolation theory.
• Next steps find the code the initiates the figures, as soon as they match start analyzing at least 5 genomic models.

[loretopaulinojr]

Try to reduce the number 5 - 10 loop in one organism.

[loretopaulinojr]

May 17, 2024 Friday Lab Meeting:

Marinova, multple chromosomes Encoded for ECRs

Encode a plasmid then conduct a growth rate