Question:
- What do you use to find the
newest literature and stay up to date in your field? y
- Can you recommend a neat
program to generate good-looking protein domain structures?
- A particularly user-friendly
primer design app?
- A clever way to make taking notes
more efficient?
- A website to draw pretty
phylogenetic trees?
- Endnote, Mendeley, or
something completely different?
- Have you found a great
online to-do list generator?
- Etc
1.
Bibliography update
I
think the principle here is what is your subject and it could be in which
database, from this you can use any tool to find right data and have a good
materials.
The
second things is your key work and search tools, if it right and correct (for
example GH61 is AA9 and what is your database, focus on gene or focus on
process -> show you the results search much more precise.
The
last things is how you treat your biblio, become a good analysis of
quantitative and qualitative.
1.1. Database
1.1.1.
What do you use to find the
newest literature and stay up to date in your field?
To build a chart trend line wit query
Scholar plot
or other field Google trends
1.1.2.
Google scholar
Easy to use alert service for newly
published research. Define your own queries (e.g. keywords that appear in the
title/abstract, author names, etc.).
(Note: Google Scholar has a similar
service, so do many other websites, like Scopus, etc. Pick your favourite!)
Research gate
Subscribe new paper form author
1.2. Citation and manage
1.2.1.
Endnote
1.2.2.
Mendeley
1.2.3.
Zotero
2.
Text edit
2.1. ShareLatex
2.2. Nopad++
2.3. A clever way to make taking
notes more efficient?
3.
Data analysis
Nifty program to generate nucleotide or
protein domain structures. Very easy to use, freeware (Windows/Mac/Linux).
Allows graphics export as SVG, PDF and EPS, so you can very easily polish the
figures in Illustrator.
Costs 10$, but it’s SO good for Mac to
easily switch between your 20 open Excel files, etc.
Makes beautiful and customisable
phylogenetic trees. Input multiple sequence alignment.
Very easy to use shading tool for multiple
sequence alignments.
Website where you can easily create your
own customised background noise soundscape to improve concentration: fire
crackling, rain, train noises, white noise. Very good if you can’t work to
music, but the environment is too distracting.
Best to-do list I have found online. You
can make a new list for each project and keep track of upcoming tasks.
Colour-tag or set due dates. You can even invite more users for a collaborative
to-do list.
3.1. Gene
3.1.1.
A particularly user-friendly
primer design app?
Generate nice sequence alignment (different
shading possible), add PDB entries to the alignment to get information about
secondary protein structures.
Biological sequence alignment editor and
viewing tool for Windows. Trimming, shading, etc. possible.
3.1.2.
A website to draw pretty
phylogenetic trees?
3.2. Protein
3.2.1.
Can you recommend a neat
program to generate good-looking protein domain structures?
Ø PyMOL
Make 3D structure
+ can write command
+ make a video
+ find ligand and protein
Freeware program (both Mac and Windows) for
visualising protein and molecule structures. You can get figures with very high
quality. Extensive wiki available. It’s possible to make videos/gifs of
molecules (e.g. zooming into the active site). Current users: Vero, Johan,
Scott, Jae.
Cazy pedia
Find the gene classify enzyme
Fugalgenomic.ca
Find sequencing of group enzyme
3.3. Data
3.3.1.
MatLab
Matlab (which is available through a
Chalmers licence) also offers many apps for various applications that have a
graphical user interface and don’t require programming experience.
For example:
·
Curve fitting app: e.g. curve
fitting for kinetic data, contour plots (3D)
·
Distribution fitting tool
·
Computational biology (sequence
alignment, phylogenetic tree)
·
For modelling of metabolic
pathways. You draw pictures of e.g. signalling pathway and put your data in à get model estimates. Both Windows and Mac.
·
Webbased tool to draw (simple)
molecules.
Notepad++
·
Text editor for windows. Very
good for programming, because it recognises different programming languages and
aligns the code properly when you open a file
·
Screen capture tool that can
capture both static images and videos. It’s possible to even annotate the
captured image.
·
(Note: Windows 10 has Snipping Tool included that does
targeted screenshots, and for Mac users Cmd+shift+4
is very useful when you want to make a screenshot of a targeted region on your
screen)
3.3.2.
Excel
Corrects typos and grammer mistakes not
only in Word, but also in Gmail, Facebook and everywhere else on the web.
Inline Charts (Sparklines) in Excel
It’s possible to make little inline charts
in Excel to see a trend at a quick glance.
Windows:
Mac:
Result:
(Note: Excel has A LOT more functionalities
than we usually use. For example under Data>Data Analysis, many statistical
tests can be done, e.g. 2-factor ANOVA, correlation, fourier analysis,
regression, random number generator, t-tests, etc.)
4.
Store and sharing
4.1. Have you found a great online to-do list generator?
-
Google calendar
-
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