TS Group: Software to Install
Quickstart: What you need to work in our group. Install all, ask labmates if you have issues.
Basics: Set operating system and all software to UK English for language and for number format (decimal point as default, not German comma); set location to Germany, currency to €, keyboard to German, date format yyyyMMdd, time format 24h, etc. See TUDD IT Accounts page to get and set up Mail, VPN etc.
Everyone: ChemDraw (browser plugins); Prism; MS Office (!set to default English, and decimal point for Excel); Zotero (plus Word plugin and browser Connector);
DropBox Client and TUDD FileShare Client; Affinity Designer (or free Inkscape).
+Online Accounts: setup group Google account on computer & phone (talks/meetings calendars; reagent ordering & contact details spreadsheets).
Active Use: see Using Software guidelines: incl. email client eg. Thunderbird or Mail; reference manager Zotero; light text editor eg. TextEdit or Notepad++ instead of Word.
Avoid for work: Endnote & Citavi; Adobe Illustrator; jpgs; nonvectorial pictures containing text; graphs from Excel.
+BioLab: FACS software (eg. flowingsoftware on Win; FlowJo on Mac); Arduino; get a Benchling bio e-labbook from JTS; FIJI (replaces ImageJ).
+ChemLab: MestreNova; Chimera/X or PyMol; get CheMotion e-labbook and GoeChem chem inventory login from OTS (replaces Open E-nventory).
Advanced:
photopharma: Arduino GUI (group programs for blinking, duty cycle);
web: FreeFileSync; FileZilla;
power use: Acrobat or a strong PDF editor; Notion (notes org.); TeamViewer;
+Adv Win: Notepad++; Foxit PDF Reader; 7zip;
+Adv Mac: Handbrake video compressor; Paintbrush; TheUnarchiver; HomeBrew; AppCleaner. For .csv handling on Mac, use Numbers; if you can't search properly in Mac Mail, check your IMAP.
Free & OpenSource Software (FOSS) for Science
- Chemical Biology: EMBL-EBI tools incl. name ↔︎ SMILES; RSC ChemSpider; OpenMolecules tools incl. property predictions / explorer, torsion angles;
- Structure Viewing: Chimera / since 2018 ChimeraX: a free great protein-ligand viewer that is now better than PyMol and is easier to install. For PyMol you can find many install guides online, or use a precompiled build like MacPyMol.
- Molecular Modelling: software for doing geometry calculations - easiest probably Avogadro and/or ChemAxon's Marvin Sketch; also Ghemical (Mopac based).
- Docking: options include Vina (or older Autodock Vina) or DOCK 6 from UCSF. FOSS Molecular Modelling software.
- TUDD FOSS software.