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New group member IT instuctions

  1. You will be given an email forwarder derived from your name, e.g. John Smith => [email protected] Please, use this email for registering to all work related services. This is just a forwarder - any email sent to @intbio.org will be frowarded to your personal email.
  2. Register on github.com with this email. Your user name should be like j-smith , or if it is taken j-smith-biomsu. NB(!) - use dashes not dots, between your name letter and surname.
  3. Please register at https://www.zotero.org . Zotero is a reference and citation manager used in our group.
  4. Send your GitHub and Zotero username and email to [email protected] . You will then get an invite to intbio organization and group on GitHub (https://github.com/intbio) and Zotero - check your email and also account pages at Github and Zotero.
  5. For communications we use slack https://slack.com . Install it . Use this link to signup to a group workspace https://join.slack.com/t/intbiol/signup . You may also get an invitation to a relevant project channel if you plan to work on a specific project - so check you email.
  6. Likely you will also get an account on newton.bioeng.ru , which will be like j_smith
  7. Likely you will also get an account on Notion. https://notion.so Register their and send info to [email protected] about your account to be added to pages.
  8. If you are doing experimental work, register on http://benchling.com . Send request to join "intbiogroup". Send email to [email protected] to request aproval.
  9. You can get login and passoword from local network and computers (ask G. Armeev).
  10. Please, send any further qestions to the #helpdesk channel in Slack!

Basic IT training

  1. Familiarise yourself with using newton https://github.com/intbio/IT_notes/blob/master/newton_cheatsheet.md
  2. Most likely you'll need to understand how to use Linux, Git, Jupyter notebooks and program in Python. Please, use this Crash course to learn it https://github.com/intbio/IntBioEdu/blob/master/ITcc.md

For students planning to do Molecular Dynamics simulations

  1. Look at the Gromacs tutorials here https://github.com/intbio/MolModEdu
  2. Start with this one https://github.com/intbio/MolModEdu/tree/master/GROMACS/nucl
  3. On github there is a repo https://github.com/intbio/gmx_template It allows you to start any simulation through a Jupyter notebook on Newton cluster. Activate the 'moldyn' kernel for that.
  4. https://github.com/intbio/IT_notes/blob/master/lomonosov.md https://github.com/intbio/IT_notes/blob/master/lomo_quick.md