Lab Mood

Pharmacoinformatics & Drug Design

Welcome to the Ramirez Lab! We are delighted to have you! Please read the following to catch up.


Lab Harmony

Please be considerate of your fellow lab mates. Some ways to do this are

  • Talk to your lab partners about the computational resources and computing time you need to use, it is important to coordinate and optimize resources.
  • The Ramirez Lab has an open source policy, which means that the codes developed in the Lab are public domain, and are intended to be shared with the entire community. Codes and scripts must be registered in Zenodo. Sharing information is the best way to work in a dry-lab.

  • Career Development

    We strive to make sure you are aware of as many opportunities as possible to help you develop into a stronger and more well connected scientist. These opportunities include writing grants, writing review articles, speaking at conferences, participating in training courses, attend career development webinars, mentoring less experienced trainees etc. Please take advantage of these opportunities to give yourself the very best chance to achieve your scientific goals.


    Scientific Integrity

    Important: Never manipulate or selectively exclude/expand data to achieve an expected or desired result. This is falsification and ignorance is not an excuse. Never use text or content from elsewhere in your writing without citing it appropriately (even if it’s something you previously wrote, which is called self-plagiarism).


    Lab Notebook and Data Backup

    Here we use Evernote and GitHub along with the Ramirez Lab webpage to take notes about the projects, meetings, ideas, etc. Also, to save the codes / scripts and any other development made in the Lab. So, your lab notebook belongs to the university and everything should be stored online in Evernote and/or Github. If you also have additional scratch notes, please take a picture and/or upload critical calulations to your online notebook.

    Please transfer all your raw data/images to the Lab server at the end of every month as well so it can be backed up.


    Software

    In our lab we use Mendeley as a bibliographic manager, GraphPad to analyze/plot data and generate graphs, and Illustrator to produce figures for publications, presentations, posters and so on.

    To perform Molecular Simulation and data analysis we use different software and servers:

  • Homology Modeling: Modeller, Schrödinger/prime, Swiss-Model, I-tasser, Rosetta, and EVcouplings.
  • Docking and virtual Screening: AutoDock vina, Schrödinger/Glide, Schrödinger/Phase, ZINC-Pharmer.
  • Molecular Dynamics simulations: Amber, Gromacs, NAMD, and Desmond.
  • Molecular Visualization: VMD, Pymol, and Schrödinger/Maestro.
  • Data processing and analysis: KNIME, Cytoscape, Jupyter, and Schrödinger/Scripts.
  • Please talk to David and contact the research assistant in charge of the software to access these resources:


    Lab Meetings

    UPDATE: All meetings are virtual until further notice due to COVID19.

    We have several types of lab meetings and the frequency and scheduling of these are based on the current needs of the lab. These meetings are mandatory unless we’ve discussed in advance otherwise.

  • Lab Meeting: Are weekly meetings of 1 or 2 hours where all members present a detailed update on their work including background, data, interpretations, and future directions.
  • Journal Club: Are meetings every 2 weeks where a person presents a paper of their choice or one of outstanding interest to the entire lab. More time should be spent on critical analysis of than on simple review of the paper. please use these guidelines to prepare this activity correctly.
  • Individual Meetings: This is your protected time with David to discuss data and anything else of concern. Meetings are ~30 minutes long and the frequency depends on your needs. Please check out this post to be prepared for your meeting.
  • Non-regular meetings: Send n email or set up a virtual meeting at any time if you need to talk for any reason.
  • Get-together: Go and have a beer with your lab mates, the ideas will flow better for sure.

  • Lab Jobs

    Everyone contributes to making the lab run and has dedicated tasks they’ve agreed to be responsible for. If you have agreed to do a lab job, please take this seriously and take care of your duties on a regular basis. It’s likely the entire lab is counting on you/waiting on you. We typically re-assign these tasks as the lab grows and shrinks.


    Need Help?

    We’re definitely in this together, but everyone is responsible for their own learning and development as well. Your first line of defense when stuck on an experiment should always be the literature (and Google). Don’t ask someone else by default if you can figure it out yourself in a few extra minutes. This is a waste of others’ time and robs you of the opportunity to learn something more deeply. Also, someone else’s information may be out of date. Your peers, more experienced lab mates, and David are also always available to you and happy to help if needed. If you’re stumped, tell someone. Good ideas often come from open discussion.


    Work Schedules

    Everyone has different levels of efficiency and experience. Also, each individual person goes through phases of more and less intense work based on deadlines and committments. Don’t worry about your labmates’ schedules. Productivity is much more important than hours. That said, please be around during core work hours (roughly 9am-5pm) so you can learn from each other and be present for meetings and joint discussions. Let David know if you will be out of the lab for a full day or more. Lastly, hard work is required to be competitive for whatever you choose for your future career, but learn to keep a consistent balance for your health and sanity. It’s a long road.


    Collaborations

    The Ramirez Lab members have a wide range of expertise and experience. We hope to foster an environment in which everyone can freely discuss and learn from each other. While we encourage everyone to participate in free intellectual exchange, everyone has their own individual project and own individual goals. Please do not ask others in the lab to perform tasks or any experiments on your project (nor should you agree to requests to do so) unless we have explicitly discussed a collaboration between you.

    We also strongly discourage hierarchical thinking. Every person in the lab is working for themselves and their own scientific/professional goals. We have made a conscious effort to give all lab members, regardless of their experience and title, ownership of their own work. Regardless of their level of education or experience, junior members of the lab are not the employees of any other lab member and should not be asked to perform experiments on anyone else’s project.

    If you have identified a potential external collaboration, fantastic! Please just discuss with David first before proceeding.


    Ramirez Lab Mood was inspired and adapted from Avasthi Lab.