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# Newcomer's checklist
### Welcome to the LCSB!
Below you can find a to-do-checklist and some practical information aiming to guide your through the first days at the LCSB together with the (corresponding people in charge) in brackets.
### To Do's
* Sign your contract (HR department)
* Attend the University Welcome Meeting: Have your picture taken for our website and get a library card for online access of publications
* Attend the LCSB Welcome Meeting: Administrative welcome presentation (communication team) & Biosafety introduction (safety team)
* Fill in the newcomer's profile for your introduction on the intranet and in the newsletter (communication team)
* Get introduced to your team members, especially to the administrative team (your godparent)
* Have your E-Mail adress added to the relevant LCSB mailing lists (your godparent)
* Read the biweekly LCSB newsletter and explore the [LCSB Intranet](https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx)
* Hand in you tax card to the HR once you received it by post (HR department)
* Get your entrance badge (your team's secretary)
### Services and Websites
You will need two accounts to make use of services and tools:
* **UNI-LU account:** To use the IT services, also known as SIU, will give you your account at your first working day
* **LUMS account:** This account is used for particular services (see below) and will be created after you have your UNI-LU account. Your godparent can assist you in that.
#### The **UNI-LU account** is used to access the following services:
* Mail services, including web mail accessible from the browser via: [https://owa.uni.lu](https://owa.uni.lu)
* Microsoft Office & Teams: [https://portal.office.com](https://portal.office.com)
* University’s Service Portal to create tickets for IT, office setup, and other issues: [https://service.uni.lu](https://service.uni.lu)
* SAP, to make leave requests, see and print payslips and other HR-related services: [https://fiori.uni.lu/fiori](https://fiori.uni.lu/fiori)
* Webex which is used for all virtual work meetings (implemented due to the COVID-19 pandemic), unless the other party requires the use of other software. You can login with UNI-LU account at: [https://unilu.webex.com/](https://unilu.webex.com/)
* University Intranet: [https://intranet.uni.lux](https://intranet.uni.lux)
* LCSB Intranet: [https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx](https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx)
* specific communication channels, such as Slack, Basecamp an others, depending on your team. Your godparent will provide you with further information.
#### The LUMS account is used to access the following services:
* Owncloud, a file cloud deployment at LCSB: [http://owncloud.lcsb.uni.lu](http://owncloud.lcsb.uni.lu)
* Gitlab, where the bioinformatics core team we manages its work products, source code and websites: [https://gitlab.lcsb.uni.lu/](https://gitlab.lcsb.uni.lu/)
* other specific and licence-dependent software that is relevant for your work
#### Enjoy your time at the LCSB!
If you have any questions, do not hesitate to ask!
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# Checklist for godparents
Thank you for accepting thegodparent role and taking the time to help him/her get started at the LCSB!
Below you can find a checklist for the first steps with this task together with the (corresponding people in charge) in brackets.
The overview checklist in .pdf-format ist avaliable [here](https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Godparent%20Checklist%20-%20newcomers.pdf).
### Tasks for the godparent
- Welcome the new employee
- Introduce the new employee to the administrative staff in order to provide him/her with:
* an entrance badge (your team's secrretary)
* office supplies (communications team)
* a computer (your team's secrretary)
 
- Show the new employee around and introduce him/her to your group and to the LCSB team
- Make sure that the new colleague receives and signs the Biosafety Information Pack before starting lab work, as all LCSB employees (also administartive staff) must be aware of the guidelines and risks of the labs.
- Explain and show:
* LCSB intranet and newsletter and UL intranet
* Uni/LCSB policies and culture: how to find details about them on the intranet
* ATLAS server structure
* Meetings at LCSB: team meeting (mandatory!), group meetings, TGIF, CETs etc.
* Infrastructure: transport, lunch, chèques repas etc.
* email signature and confidentiality disclaimer
* business cards (to order them contact your group’s team secretary)
 
- Make sure the new employee is added to the relevant email lists. For this please [open a ticket at ServiceNow](https://service.uni.lu/sp), mentioning the name and **email address of the new employee** and the **email addresses of the required email lists** that he should be added to.
- For details, see the LCSB Handbook on the intranet.
### Thanks for your help!
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# Godparents for Newcomers
Please also consult the [checklist for godparents](https://howto.lcsb.uni.lu/?hr:newcomers:checklistGodparent).
### Summary
In order to help new employees to easily integrate in their new workplace and senior members to better know and understand the new colleague, each new employee will be assigned a "godparent".
### What is a godparent?
Being a godparent is a voluntary function within the LCSB.
A godparent is as a person who, through its experience at the centre and in Luxembourg has gained an extensive knowledge about procedures, rules, corporate culture etc. and who desires to help others, advice new colleagues when they arrive in Luxembourg and who desires to build new relationships.
### What should a godparent do?
A godparent is free to organise and build the relationship with a new employee. However, the following task should be covered.
* Welcome the new employee
* Show the new employee around and introduce him/her to the team and to other LCSB/ Uni.lu members: most importantly to the administrative in order to provide a badge, office supplies…
* Make sure that the new colleague receives and signs the Biosafety Information Pack, as all LCSB employees must be aware of the regulations and risks of the labs
* Explain Uni/ LCSB policies and culture
* Make sure the new employee is added to the relevant email lists. For this please [open a ticket at ServiceNow](https://service.uni.lu/sp), mentioning the name and **email address of the new employee** and the **email addresses of the required email lists** that he should be added to.
* Make sure the newcomer gets access to ATLAS as appropriate.
Duration of godparenting: Minimum 2 months and no longer than 6 months.
### How to become a godparent?
All LCSB members are eligible to become godparents. There are no minimal qualifications required, mentors must only work for at least 6 month at the Uni.
However, in general HR in collaboration with the LCSB’s administration team will shortlist few potential candidates. Potential candidates shall be contacted and asked if they accept the function. In a case of refusal the next candidate on the list will be contacted.
Preferred candidates for this assignment are members of the same unit or project, a relevant research field, or the same hierarchical level. To avoid conflicts of interest, in principle PI or superiors are to be avoided as godparents.
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# Onboarding new members at the LCSB
## Purpose
The LCSB regularly welcomes newcomers who have just joined one of the research groups or the support teams.
The on-boarding process aims to ensure their smooth insertion within their group and within the LCSB.
It completes the introduction at the Welcome Day of the university by providing information specific to the LCSB.
On top of practical information, this process should convey the LCSB values and the way we all work together.
## 1. Godparents
When a new member joins the LCSB, his team should assign him a godparent who will guide him during the on-boarding process.
The group PI are asked to nominate a senior member of the group as “god-parent”.
The godparent should show the newcomer around the LCSB premises, introduce them to all the relevant LCSB staff (help for networking during social events), and take care of some of the early procedures such as:
- prepare a desk
- get a computer
- get phone
- show how to get office supplies
- register for mail lists
- explain Uni/LCSB intranet, services and [important links](https://howto.lcsb.uni.lu/?general:links)
- introduce to the team
- explain the lunch voucher system and where to get food
## 2. Welcome meetings
- **University Welcome Day**: The newcomers have to attend the University Welcome Day to get a general overview of the university and have their official picture taken for the website.
- **LCSB Welcome meeting**: Once a month a two hours meeting is organised at the LCSB for the members who arrived recently. During the first part, a round table allow participants to introduce themselves and to place their “location sticker” on the LCSB map in BT2 staircase. Then, a member of the communication team presents the LCSB, its goals and values, and provides some practical information (who’s who, basic procedures, where to find answers, etc.). The second part is dedicated to security and safety (building evacuation, emergency exits, lab safety…).
The participants also get a copy of the LCSB annual and research reports and the slides used during the meeting are shared. The newcomers receive a calendar invitation for this meeting, sent by the communication team.
In order to introduce the newcomers to the whole LCSB team, the new members are mentioned in the LCSB newsletter (Photo, name, position and email address in the “Newcomers” section). They can also introduce themselves during the weekly team meeting at the LCSB.
## 3. Checklist for administrative tasks
- Get entrance badge at the Maison du Savoir (Security office on 2nd floor). Check with your team secretary what kind of access you have (rooms and hours) and how to update it if needed.
- Get acquainted with your colleagues, especially your group, the group secretary and the administrative team. The godparent should show the new employee around and introduce them to the LCSB team.
- Get access to the relevant mail lists (LCSB-Team + group list). The godparent should open a ticket in ServiceNow mentioning the name and the email address of the new employee and the required email lists that they should be added to.
- Familiarise with different LCSB tools: ATLAS server (to get access, [open a ticket in service now](https://service.uni.lu/sp)), the regular meetings (team meetings, TGIaF, CETs), the lunch vouchers distribution, etc. The godparent should explain how things work at the Uni/LCSB (policies and culture).
- Fill in the profile on [LCSB intranet](https://intranet.uni.lux/the_university/lcsb/lscb_internal/). Check that the information on the personal webpage on university website is accurate and that the newcomer is mentioned in LCSB people list and in the group member list on the website.
- Set up the proper email signature and confidentiality disclaimer for your university mailbox: [Guidelines on the intranet](https://intranet.uni.lux/the_university/sc/Lists/Policies%20%20Procedures/DispForm.aspx?ID=9)
- Order business cards through your group’s secretary if needed.
- Read the biweekly LCSB newsletter and explore the intranet to stay up to date with what is happening at the LCSB. Send an email to the LCSB communication team if the newcomer hasn’t received it after a few weeks.
- Complete your trainings to get further access to the labs. The godparent should make sure that the new colleague receives the Biosafety, Data Management and Data Protection Training before starting lab work, as all LCSB employees must be aware of the guidelines and risks.
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# Add a .gitignore to your repository
The version control system git tracks all files in a repository.
Sometimes, you do not want certain files or directories to be tracked, but fully ignored by `git`. These files or directories
can include binaries, images, dependencies, log files, or analysis results. Also, hidden system files are usually picked up by `git`.
The idea is to create a file named `.gitignore` that lists all the files and directories that should be ignored by `git`.
For instance, in order to ignore all log files with the suffix `.log`, the content of the `.gitignore` file should be:
```
*.log
```
A common example is to ignore system files as well, such as the `.DS_Store` file:
```
.DS_Store
```
*Note:* Sometimes, you might not see the hidden system files. You can do so by browsing to the directory in the terminal and typing:
```bash
$ ls -lash
```
Once the `.gitignore` file has been created, you can add and commit the file as any other file in the `git`-tracked repository. A relatively complete collection of `.gitignore` templates can be found [here](https://github.com/github/gitignore).
More information on the `.gitignore` mechanism can be found [here](https://www.atlassian.com/git/tutorials/saving-changes/gitignore).
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# Publish a repository
By default, the repositories created on the LCSB Gitlab are private, i.e. they cannot be seen by anyone outside LCSB.
In order to change the visibility of the repository, you can do so by browsing to `Settings` and then expanding the section on `Visibility, project features, permissions`.
There, you can set the visibility to `Public`. It is important to note that the group must be public in order to change visibility of the repository.
Remember to follow the [LCSB policy regarding code development](https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-07). In case of questions, please do not hesitate to contact the [R3 team](mailto:lcsb-r3@uni.lu).
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# 10 ways to improve your English
Francisco ARAGAON ARTACHO, former postdoc in the Systems Control group, has made a list of the ten most important points that helped to improve his English. In this article he shares them with you and explains what he means by each of them.
**1. Believe improving your English is something very important**
I think this is the most important point. If you don't believe a good written English is important, you will never improve it. So... why is it important? The way you write will give your reader a first impression about you. Even more, the reader will even get an impression about your personality (tidy / messy / arrogant / smart / knowledgeable / dumb). He / she probably doesn't know you, nor knows how good your ideas are. Don't give him / her a bad first impression: it will be hard to change his/her mind. While refereeing, I've directly rejected several papers because the English was terribly bad, or because it was full of typos. Nobody wants to read a text with many typos and which is clearly against the "golden rule" to never make a referee angry! Before submitting a paper / grant proposal, check it carefully. If one of your co-authors is a native English speaker, ask him / her to check the grammar of what you wrote. If not, ask a friend. If possible, wait for a week and read it again. You will probably discover that what you wrote is not as nice as you thought. You will find many typos and errors.
**2. Read**
Read as much texts in English as you can, especially novels. If you read good writers, perhaps (probably) something good will stick in your mind. Try to use their "fancy words and sentences" whenever it is possible.
**3. Listen**
I believe listening to music and watching movies / TV shows helped a lot to improve my English. Even during the most boring talk at a conference you may learn something good for your English.
**4. Use synonyms**
Synonyms are good. Avoid repeating words / structures whenever is possible. Use as many different sentence connectors as you can / know. Your text will look better and will be nicer to read. I normally use [Thesaurus](http://thesaurus.reference.com/).
**5. Use a dictionary**
While writing, I always have a dictionary open in my browser. I especially like [wordreference.com](http://www.wordreference.com/), which even has the British / American pronunciation for many words.
**6. Check what Google says about your sentences**
If you're not sure about a sentence you wrote, google it (or part of it), using quotation marks. If there are only a few hits, your sentence is probably wrong. If you doubt between two versions of the same sentence, the one with more results in Google is probably going to be the correct one.
**7. Write short sentences**
Long sentences make the reader feel exhausted, so do your best to avoid them. Try to punctuate correctly: use commas, colons, and semicolons.
**8. Write short paragraphs**
In a similar way to the previous point, long paragraphs are exhausting. I remember that when I was a kid I hated books without "white space" (breaks), and I guess I still have some similar feeling. A text with short paragraphs always looks easier to read at first glance. Additionally, while aiming to write short paragraphs, you will be forced to structure your ideas (next point).
**9. Structure your thoughts through the text**
Structure your ideas to explain yourself. It is very important to use sentence connectors, as for example: moreover, however, besides, although, nevertheless, in spite of, then, therefore, thus, hence, whence, on one hand / on the other hand, additionally, further, furthermore, otherwise...
**10. Ask people to correct you**
People (wrongly) believe that it is impolite to correct others when they're not speaking in their native language. I guess this happens because no one likes to be wrong, and even less to be pointed out for being wrong. At the beginning, when I started learning English, people used to correct me very often. Unfortunately, as soon as my English was "good enough", I noticed that I was getting less and less corrections, despite my English wasn't that good. For example, only last year my Aussie housemate told me that I was pronouncing "yellow" wrong (and, probably, every single word starting with "y" - pronouncing it like "j" in "jelly") because he wanted to piss me off. At that moment I guess he was disappointed to see that I liked to be corrected, but he started telling me my mistakes since then. Thus, if you want to be corrected you'll need to ask the others to do it, and remember to thank them with a not-very-fake-looking smile when they do it :).
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# Publishing a tool in *bio.tools*
First, *bio.tools* serve two main purposes:
- dissemination of your tools
- collecting systematic and reasonable statistics about the available
software for many purposes, including data science and performance reports
To get your contents in, you need to fill an application and get an account.
Filling out the application is particularly straightforward.
After you get the account, you can click "Add content" in the "Menu" on the top
right, then go through around 10 tabs that allow you to fill lots of
interesting information about your tool, and finally submit it, which makes the
contents immediately visible.
This card collects some reminders about what you should not forget while
submitting the tool, perhaps useful as a checklist.
## General tips
### Use search and consult the curation guide to resolve ambiguities
The guide is currently here:
https://biotools.readthedocs.io/en/latest/curators_guide.html#summary-group
It includes helpful and authoritative guidelines for almost all fields that you
can fill, including examples.
As the last resort when you do not know what to do with a field, you can try
search suggestions in the structured search box above, and try to be at least
consistent with the rest of the database. In the search box, type in a single
letter, wait for a moment (or press arrow down), choose the annotation
category, and see what others have used.
### Add a "backup" maintainer
This may remove a lot of unnecessary workload from you, and will help everyone
at times when you are not available. (Or, at least, reduce the stress levels.)
### Add _many_ links to all types of documentation
This helps in two ways:
- The search engines will be able to categorize and index your contents better,
possibly giving more helpful links to your tools.
- Users of *bio.tools* will be able to explore the most relevant parts of your
documentation very quickly, helping them to make a faster decision about
using your tool. For example, it is often a relief to quickly see that a
bioinformatics tool has an explicit step-by-step tutorial, and that a web
visualization framework has a complete useful API reference.
Include the (interesting) relations to other tools. This adds a bit more
interesting data to both search engines and statisticians who process
*bio.tools* content, and gives an documentation of possible "use-cases".
## Proper labeling
### Choose the bio.tools ID correctly
As the name says, the "Persistent biotoolsID" cannot be changed. It will be
permanently displayed as an identifier in almost all content that is
autogenerated from *bio.tools*. For users, that concerns mainly the URLs, so
you may want to apply similar formatting guidelines as for URLs (use hyphens
`-` instead of underscores `_`, do not use capital letters, ...).
### Add your tool to proper collections
Collections group the results of various larger cooperated (or loosely
organized) efforts, such as "Galaxy tools", "Parkinson disease research", and
"3D BioInfo".
If your tool is related to ELIXIR, you should fill in the correct ELIXIR node,
platform, community _and_ collection. Remember to:
- Add _all_ involved ELIXIR nodes.
- **Add your tool to the node-specific ELIXIR collections.** For LCSB, that is
usually **ELIXIR-LU**. This is counter-intuitive and seems duplicate to the
categorization by ELIXIR nodes, but:
- at least 2 nodes use collections labels instead of node labels to scrape
data about their tools
- there is search support only for the collections; currently (March 2021) it
seems that you cannot easily search for tools by ELIXIR nodes
### Fill in the tool "Function" very verbosely
The main reason for categorizing tool functions is to provide a systematic way
for listing the tools in topic-based catalogues that can be browsed by users.
The categories and data formats available for describing your tool function
rarely give a precise match. That is okay, you can choose a broader category.
Use all categories that match even a small part of your tool; it will
potentially help *bio.tools* users to find your tool even if they do not know
what precisely they are searching for.
Selecting a very specific category ("deeper" in the topic tree) also implies
all "parent" categories, so you do not have to be afraid of over-specification.
*Bio.tools* search box will automatically include your tool in searches for the
broader categories.
## References and publications
### Be comprehensive about publications
Add _all_ publications where you described, showcased, and benchmarked the
tool. Also add preprints.
There are several purposes for the precise publication tracking:
- the users may (and often will) sort the tools by the citation count, likely
trying the most tested approach first
- the publications provide an additional form of documentation (often more
colorful than the API docs)
- the links and citation counts provide a nice, easily available statistic
about ELIXIR performance
### Use the Credit tab
The purpose of the "Credit" tab is not immediately obvious -- basically, you
can credit anything that has helped you with creating the tool. This is
currently used for at least 3 purposes:
- systematic tracking of non-ELIXIR collaborators (add ORCIDs)
- listing the **industry partners**
- listing affiliations to particular research institutions
(**remember to add LCSB**)
......@@ -5,7 +5,7 @@ order: 1
---
{% comment %}
The Bioinformatics Core and Lab Support teams assist researchers from the Luxembourg Centre for Systems Biomedicine ([LCSB](https://www.uni.lu/lcsb)) with the organization, management, and curation of research data through its R3 initiative.
The Bioinformatics Core and Lab Support teams assist researchers from the Luxembourg Centre for Systems Biomedicine ([LCSB](https://wwwen.uni.lu/lcsb)) with the organization, management, and curation of research data through its R3 initiative.
The How-to cards are intended to provide practical guidance in implementing Data Management, Data Protection, IT setup, lab support, and others.
{% endcomment %}
......@@ -17,6 +17,12 @@ The How-to cards are intended to provide practical guidance in implementing Data
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"link": "{{ '/cards#general' | relative_url }}"
},
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"title": "On&Off boarding",
"caption": "A new colleague joined or my current colleague will leave. What do I have to do?",
"icon": "<i class=\"large material-icons\">compare_arrows</i>",
"link": "{{ '/cards#on-offboarding' | relative_url }}"
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"title": "Access",
"caption": "How can I get access to systems and infrastructure?",
......@@ -29,6 +35,12 @@ The How-to cards are intended to provide practical guidance in implementing Data
"icon": "<i class=\"large material-icons\">add_circle</i>",
"link": "{{ '/cards#contribute' | relative_url }}"
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"caption": "Guidelines regarding backing up your data",
"icon": "<i class=\"large material-icons\">backup</i>",
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......@@ -47,6 +59,18 @@ The How-to cards are intended to provide practical guidance in implementing Data
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"link": "{{ '/cards#lab' | relative_url }}"
},
{
"title": "Publication",
"caption": "I want to publish my article",
"icon": "<i class=\"large material-icons\">menu_book</i>",
"link": "{{ '/cards#publication' | relative_url }}"
},
{
"title": "PPC",
"caption": "I need information on the pre-publication check (PPC)",
"icon": "<i class=\"large material-icons\">fact_check</i>",
"link": "{{ '/cards#ppc' | relative_url }}"
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