News and Views from a Mass Spectrometry Lab in Irapuato, Mexico

Rule your Inboxes with RAcS (Read/Action - Spam)

Monday, Monday. You are eager to work on a manuscript. But you have to attend four hours of seminars. And the Email inbox is populated with 127 new messages! If you now start classifying, reading, deleting, and answering Emails, you are not a scientist but a receptionist.

Understanding your Email traffic

Email is currently the most used medium in business communication. It replaced paper letters and fax. You can send large documents quickly and safely. Thus, Email is hard to ignore, and people (ab)use this channel to get your attention or to send you homework. To separate the wheat from the chaff with automated filters, we first need to analyze incoming messages. Initially, I classified them into five categories: 

  • Information - Emails that contain useful information, but do not require immediate action.
  • Spam - Spam includes all types of undesired communication, such as commercials, scam, social network notifications, and extensive mailing list discussions.
  • Homework - Messages that need my attention and response in a reasonable time.
  • Conversation - Exchange of ideas and opinions with one person or a group.
  • Urgent - Emergencies that need my fast decision or intervention.

After careful thinking, I reduced the categories to:

  • Read/Action (=Ham): The Emails you need to read because they contain essential information or require your action.
  • Spam: The Emails that you can safely ignore.

This binary classification facilitates the automated filtering of messages by artificial intelligence (explained below).

Unifying inboxes and Contacts

You probably use more than one Email account and different devices. Unifying inboxes simplifies the organization of your data. Thus, I tested various commercial and free Email programs supporting multiple IMAP accounts and a unified inbox (Evolution, Mailpile, Mailspring, Nextcloud Mail, Rainloop, Thunderbird). Finally, I chose the web client Cypht, which I installed on a virtual personal server (VPS). Therefore, I can use the same interface and information on all internet devices. 

On Android, I made good experiences with K-9 mail. K-9 mail also implements OpenPGP (https://www.openpgp.org) for Email encryption and verification. Of course, nobody cares about privacy.

I store contacts manually using a private LDAP server. This solution is more laborious than using Google contacts and automated address books. However, Cypht provides LDAP integration, and maintaining valuable contact data is worth the effort.

Technical helpers

Warning: This section is for computer nerds. Ordinary people activate the spam filtering of their Email provider and move to the Habits section below.

Advanced spam filtering

Too many undesired Emails still passed my providers' (IONOS, Microsoft Office 365 Outlook, and Gmail) filters. Thus, I needed a more sophisticated tool. The Apache SpamAssassin provides a rich set of efficient spam filtering methods, such as DNS and URI blacklists and Bayesian filtering. 

I installed IMAP Spam Begone (ISBG) on my VPS. ISBG checks the IMAP accounts every 15 minutes and moves messages above the defined score threshold to separate spam folders.

By default, the SpamAssassin efficiently removes real spam, such as phishing scams and commercials from suspicious servers.

However, there is still another source of spam: Internal discussion lists, social network notifications, newsletters, and product information, i.e., messages from reliable senders, but with irrelevant content. You can train the Bayesian filter of SpamAssassin with Spam and Ham messages. For this, I created a separate SpamAssassin Email account with Spam and Ham folders. I move Emails that belong to one of those categories into these folders, and SpamAssassin scans them daily (cronjob 'sa-learn') to improve its classification performance. After some training, most bothering Emails get eliminated.

Archiving and clean-up

You can boost the performance of IMAP accounts by archiving and deleting obsolete Emails, e.g.:  

  • Save Emails older than 180 days locally, and delete them on the IMAP server: Folders InboxSentHam
  • Delete Emails more past than five days: Spam folders

Both tasks can be performed with the program 'archivemail', creating one mbox file for each archived folder. The Email archives are backed-up on a remote server. Note: Probably, this archiving strategy is paranoic. 

Habits

The ISBG/ SpamAssassin eliminates most of the automated mass Emails. 

Now we have to adopt effective habits:

  • Unsubscribe Email newsletters and notifications. Do not fetch RSS feeds with your Email client.
  • Don't worry about urgent Emails you might miss. If something is really vital, people will find you. 
  • Be careful about accepting homework. If a student sends you a Ph.D. thesis on Friday, because (s)he needs the corrections on Monday, you got all the weekend! If possible, delegate work.
  • Avoid Email chatting. "It shouldn't take 30 emails to schedule a 30-minute meeting" (https://doodle.com/).
  • Don't waste your time with sloppy Emails. If the subject seems relevant, ask for complete information.
  • Check your Inbox only once/day. This rule is a difficult one but increases your productivity. You might consider even larger intervals.
  • Write concise Emails. With a descriptive subject, the adequate recipients, and a precise definition of expected feedback.

My Email workflow is:

  1. Move obvious spam messages to the Spam training folder of the SpamAssassin.
  2. Glance through and delete informative Emails.
  3. Read Emails with relevant subjects.
  4. Flag Emails that need your answer or action. 
  5. Answer flagged Emails. Give preference to well-prepared tasks, such as quick yes/no decisions, or documents ready to sign. People will learn.  

Congratulations!

Did you follow this strategy?

Great!

Your incoming Emails reduced significantly (-75%). As well, you drastically shortened the time you spend reading and answering messages.

Now, stay firm and educate people to use Email wisely!


Switching to a dumb phone

Smartphones are fantastic pieces of technology. Initially, the idea was to combine a music player with a mobile phone ("It's the best iPod we've ever made!"; Steve Jobs at the presentation of the iPhone, 2007). 

Now, smartphones are portable multimedia computers, and we use them for messaging, emails, banking, navigation, social media, sports, web browsing, and shopping.

On the downside, smartphones intruded all aspects of our professional and personal lives. In fact, job and own time cannot be clearly separated anymore, because one is expected to be available 24/7 for 'emergencies.' There is a great temptation to quickly check incoming notifications, news, or emails when waiting for the bus or feeling alone. Most of this information is junk, but anyway, there is a high motivation to frequently look at the display of the phone because otherwise, we could miss something important.

Tristan Harris, a former 'product philosopher' at Google, compares smartphones with a slot machine. The users' attention is the modern currency, and smartphones and their apps are designed to keep us staring at their displays (Spiegel International, 2016). Important factors of phone addiction are also the social networks and their feedback mechanisms, which provide us with irregular kicks and stimulate our reaction (e.g., to press the 'Like' button; please find recommended literature below). 

I had canceled Facebook and WhatsApp about two years ago because the communication was too superficial and fragmented for me. Besides, the use of my personal data, interests, and contacts for marketing is troubling me. I became (even more) skeptical about current practices when I was asked by Google: "How was the bar xxx you visited [with your friends] two hours ago?". Sure, I can contradict the use of localization data. But the apparent custom to monitor our habits with the smartphone clearly demonstrates that the consumers are the product in this business.

I realized that the smartphone needs a lot of attention (charging, updating, checking stuff, searching apps) and that I had become an addict. And I wanted to do something about it. Ironically additional apps help you analyze and optimize your habits. However, I decided on a more straight-forward withdrawal therapy:

Day

  1. Remove the phone and the charger from your sleeping room.
  2. Erase all social network and news apps from your smartphone.
  3. Erase all email apps from your smartphone.
  4. Get a dumb phone (I got a Nokia 3310 3G now) and use it.

App replacements

Maybe, you need your smartphone because of a critical app xx. However, I am quite sure that there are alternatives for most programs. Here are my app replacements:

  • Calendar: I bought a paper calendar with a week overview. It also serves for task management and making short notes. I would bet that it outperforms electronic calendars.
  • Time: I got three different wristwatches. Two of them are solar-driven, and one is mechanical. None of them got external communication (Bluetooth, WiFi), of course. A watch is essential to avoid the regular looking at the mobile phone display.
  • Navigation: On the road, we got a car GPS and, for really rough expeditions in remote areas, a manual Garmin etrex Vista HCx GPS. BTW: you can create maps with my script: https://bitbucket.org/lababi/mexico-garmin-map/).
  • Alarm clock: We are using a radio clock with an SD card slot and a USB with thousands of Jazz MP3s.
  • Audio player: The Nokia 3310 3G got an audio player. However, in the evening and in the gym, I use an MP3 player.
  • Podcasts: Collect and download with Cloud Caster and listen to them with an MP3 player.
  • Camera: The Nokia 3310 3G got a simple camera. For high-quality action photos and videos, I got a GoPro.
  • Reading: Tolino ebook reader.
  • Uber: You can schedule rides from the Uber website. Or stop a taxi.
  • Fitness tracking: None. Just bike, walk and lift some weights.
  • Anything else: PC or Chromebook.

Experiences after two weeks

The functions of the phone and the layout are mostly predefined, and therefore I could start without any app installations. My only customizations were the uploading of a solid black wallpaper and some ringtones that I played with my trumpet. 

Contacts are stored on the SIM card or the phone (no cloud sync!). 

Since the phone has real keys, dialing numbers is fast, and you also can define speed-dial contacts. Maybe I am getting old, but I prefer keys over wiping around on a touchscreen. Making or answering phone calls is more straight-forward with physical buttons. 

I can use the phone for more than a week without charging. Considering the smaller battery, I reduced the energy consumption for the phone by about 90%. Using the Moto G5, I realize the heat it is producing compared to the Nokia.

Contrary to what I feared, I do not feel disconnected. The Nokia 3310 has an Opera mini browser, and accessing the internet is theoretically possible. But the display of 2.4" and the limited compatibility with modern websites makes surfing painfully inconvenient. You would use it when searching for an anti-poison of the animal that just attacked you. But in general, I would call the internet capabilities of this phone a placebo function.

I am still a massive computer and internet user, but I am not always connected anymore and feel more independent. Switching the phone off in the evening is simple, and I don't feel guilty and have some real free time. And I feel more satisfied crossing out tasks with the paper calendar than with my electronic calendar.

What happened to your smartphone?

The latest official upgrade for my smartphone, a Motorola Moto G5 (https://en.wikipedia.org/wiki/Moto_G5), is Android 8.1. The hardware still works perfectly, but since the current Android version is 10, the operating system is becoming obsolete soon. Thus, I unlocked the bootloader and installed TWRP and the open Android version LineageOS. Finally, I rooted the device with Magisk. Now, the smartphone holds the most recent Android version, and I got superuser powers. But be warned: You only should do that if you are technically confident and if you take the risk of eventually bricking your phone.  

In its new life, the G5 serves for GPS-navigation (https://osmand.net), as a camera (upload to Google Photos), and as a phone for traveling (dual SIM, LTE). I only installed the essential apps, and most of the time, the smartphone is stored in the draw. 

Conclusion

The integration of excessive functions into a single phone could turn out as an aberration of technology. The increasing size of smartphone displays and their high computational power are contradictory to the original idea of portability and the necessity to reduce energy consumption. High-value, focussed work and quality communication are hindered by smartphones, because of constant distractions by notifications and information clutter. 

Fortunately, it is easy to escape the social and technological pressure caused by smartphones, as my positive experience demonstrates.

What comes next?

Since my phone needs much less attention now, I got some extra time to optimize emailing!

Book recommendation

Cal Newport (2019), Digital Minimalism: Choosing a Focused Life in a Noisy World; Published by Portfolio (Penguin Random House),

https://www.calnewport.com/books/digital-minimalism/


My Sabbath Year (2018-2019)

"25 The Lord said to Moses at Mount Sinai, 2 “Speak to the Israelites and say to them: ‘When you enter the land I am going to give you, the land itself must observe a sabbath to the Lord. 3 For six years sow your fields, and for six years prune your vineyards and gather their crops. 4 But in the seventh year the land is to have a year of sabbath rest, a sabbath to the Lord. Do not sow your fields or prune your vineyards. 5 Do not reap what grows of itself or harvest the grapes of your untended vines. The land is to have a year of rest. 6 Whatever the land yields during the sabbath year will be food for you—for yourself, your male and female servants, and the hired worker and temporary resident who live among you, 7 as well as for your livestock and the wild animals in your land. Whatever the land produces may be eaten." (Leviticus 25:1-7, New International Version)

Half a year after returning from my sabbatical year, I believe having enough distance to write about my experiences.

What is the idea of a sabbatical?

Time is our most precious good, and as successful scientists, we tend to optimize our efficiency and output. Since we finish more and more work in less time, we are famous victims for accepting even more responsibilities (e.g., in editorial boards, teaching, funding review activities). We continue this vicious cycle until any little disturbance (unexpected visitors, traffic jams, internet problems, canceled school classes) causes us a high level of stress. The increasing pressure to publish ("a lot and high impact," of course) and to find funding keeps us busy. We can hold this rhythm for several years without slowing down. However, our family, social, and cultural life suffer if we answer 'important' Emails at night. And since we never learned how to shift down and reduce our speed, we are in danger of overheating and burn-out.

A sabbatical break gives us the chance to leave the hamster's wheel temporarily and to recharge batteries. And in the best case, we learn strategies for a more sustainable life.

The offer by our institution

Our research institution, The Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV) allows us to work every seventh year in another institution. The procedure is pretty simple, and during our sabbatical, our salary is fully paid. Our institutional duties, such as participation in committees, are paused or reduced to a minimum. We have complete freedom to choose a country and institution for a stay of one year.

Our host 'Max Planck', teaching and research

My wife Laila Pamela Partida Martínez and I were accepted as visiting scientists by the research groups of Ian Baldwin and Ales Svatos, respectively, at the Max Planck Institute for Chemical Ecology (Jena, Germany). Many thanks to them for their hospitality!

The MPI has all the infrastructure you can dream of. Thus, I did some experiments, e.g., mounting our 3D-printed low-temperature plasma (3D-LTP) probe on a Prosolia DESI platform (the MPI workshop built a little adaptor for me). Since I connected our 3D-LTP probe for the first time to an Orbitrap mass analyzer, I was quite happy with the analytical resolution. At least one paper should be coming out from that. As well, I had the opportunity to visit my collaborator of the BAM Berlin in our joint Conacyt-DFG project, Jens Riedel. It was awesome to see his laser toys and gadgets. However, my main research activity was related to mass spectrometry data processing and data mining. For example, I learned how to employ Docker for mass spectrometry workflows and how to post-process prot.xml files with Python.

Further, I participated in giving a course in "Computational Mass Spectrometry" for the "International Max Planck Research School (IMPRS)" students. The interaction with the group also allowed me to test an R script for XCMS and a chapter for the RSC book mentioned below.

I enjoyed the international atmosphere (especially in the coffee room), and I made new contacts. The collaboration with the ICE mass spectrometry group is ongoing, especially with Natalie Wielsch (thanks for all the chocolate!), an expert in plant proteomics.

Family and daily life

Our boys were 8 and 11 years old when we moved to Jena. Both grew up in Mexico; thus, their German language level was modest. Fortunately, they were accepted by the Montessori School Jena. We appreciate all the support from their teachers because the children were quickly integrated and made great progress. Both countries accepted the completed school years of the other country. Of course, some classes were different. E.g., the Thuringian kids have to know the alibi name of Martin Luther while he was hidden in the Wartburg - 'Junker Jörg.' In contrast, Mexican kids learn about the battle of Puebla, which is celebrated on the 5th of May. But since the Montessori philosophy is based on the inherent curiosity of children and guided activities, the kids were optimally promoted.

Before the sabbatical year, we sold our car, and in Jena, we bought used bicycles. The weekend shopping was limited to the capacity of my bike trailer, which helped to prevent the buying of unnecessary stuff and junk food. During the wintertime, biking was not always pleasant. Especially for going to school (~6 km). Nevertheless, the boys were pretty tough, and only on some icy days with snow on the road, they used the bus. In the beginning, we accompanied the children when biking to school. But later, they moved independently in the city.

It was a change for us, to live as a family of only four, without close-by grandparents or 'helping hands.' Therefore, we had to organize cooking, household, and laundry. However, it can be quite productive to stay at home for soldering a prototype, writing or programming, waiting until the washing machine is ready, and the cloths can be hanged for drying (either in the drying room or outside in the garden!).

Since we had a park and playground (Friedensberg, Jena) just in front of our house, we frequently played soccer and frisbee. Unfortunately, just going out to play is not so easy in Irapuato because we need to go by car to fields for outdoor sports. As well, we had more family time during our sabbatical year, which we enjoyed a lot.

As well, I learned shaving with a straight razor, and some days I left the bathroom with a cut. However, now I am free of expensive and waste-creating system razors!

Traveling between continents and maintaining two houses is, of course, somehow costly. Nevertheless, this was not too critical, because several services we pay in Mexico, e.g., the school, were for free in Germany. The health insurance was kind of challenging. Finally, we contracted private health insurance with coverage abroad in Mexico. Importantly, many countries got tax laws for temporal academic stays. The Jena Finanzamt (taxation office) was very helpful in resolving our questions for avoiding double taxation. In general, the authorities in Jena were very helpful for all our administrative tasks (registration/ migration/ taxation/ school, etc.). Anyway, before moving with a family, one should consider several months of planning.

Friends, culture and social life

I studied my first degree in Jena, and my wife and I came back for Ph.D. and PostDoc. Thus, we already knew many people, which facilitated our re-integration. For example, our friend Agnes borrowed us an electronic piano for the year and we made several weekend trips with her family. Thanks a lot, Agnes!

Arriving at Jena, I started again playing the trumpet. When I was a student, I was a member of the Dixielanders. 'Duddle,' their former tuba player (and now a member of BlechARTig quickly 'contracted' me for some Christmas combos. The same Duddle now will visit us in Irapuato; during his sabbatical world travel.

As well, I participated in the Max Planck orchestra and the Bavarian Musikkapelle Emmerting, where I was a co-founder more than 30 years ago, and practiced improvisation.

From time to time, I met old friends to discuss life with a beer (or two), or to watch a horror movie.

Since everything is close and well-connected in Europe, we organized a reunion with our friends from the time we studied our Master's in Birmingham, UK. We met in the house of an Italian friend that is now married to a Belgian. Our other friends came from France, England (married with a Mexican), and Indonesia. We enjoyed Belgian beer and chocolate, and we had a great time. Thanks, Susi & the Brummy family!

During the sabbatical, I also found out that Yoga is not for me ;-).

Book writing

For several years I wanted to start a Wiki about mass spectrometry (MS) data processing. I published an open-access article on biological MS workflows and advanced statistics (PeerJ, 2015), but never managed to compile a comprehensive work.

Thus, as Marek Domin (Boston College, US) asked me if I wanted to edit a book on Metabolomics for the Royal Society of Chemistry, I immediately accepted. The first draft of the book proposal I wrote on my cell phone, waiting for the kids, on a bench close to the Montessori school. Fortunately, it was summer (2018). Finally, we expanded the scope and also included Proteomics and MS data processing toolkits.

I warmly thank all the authors that contributed to the book (in the order of appereance): Magnus Palmblad, David S. Wishart, Joanna Godzien, Alberto Gil de la Fuente, Rupasri Mandal, Rahmatollah Rajabzadeh, Hamed Pirimoghadam, Carol Ladner-­Keay, Abraham Otero, Coral Barbas, Marc Vaudel, Miguel Reboiro-­Jato, Daniel Glez-­Peña, Hugo López-­Fernández, Oliver Alka, Timo Sachsenberg, Leon Bichmann, Julianus Pfeuffer, Hendrik Weisser, Samuel Wein, Eugen Netz, Marc Rurik, Oliver Kohlbacher, Hannes Röst, Tomáŝ Pluskal, Ansgar Korf, Aleksandr Smirnov, Robin Schmid, Timothy R. Fallon, Xiuxia Du, Jing-­Ke Weng, Laila Pamela Partida-Martí­nez, Bo Wen, Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Zhi Sun, Michael H. Hoopmann, Robert L. Moritz, Kaikun Xu, Cheng Chang, Cesaré Ovando-­Vázquez, Nils Hoffmann, Yasset Perez-­Riverol, Olivier Sallou and Björn A. Grüning.

Now, in March 2020, finally, the book is available from the Royal Society of Chemistry with the title "Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide."

I am very proud and satisfied with the book, and much appreciate the support of all authors, Marek and the RSC (Janet Freshwater and Katie Morrey). Writing my first textbook was a fantastic experience!

Technology transfer and product development

In 2018, my wife and I created a spin-off company (Kuturabi SA de CV) for facilitating the technology transfer of our labs, such as the Open LabBot, the 3D-LTP, and our ambient ionization mass spectrometry imaging system. During the sabbatical year, I met future collaboration partners and experts for the technical requirements of electronic devices in the European Union.

Further, I started playing with Arduino and Wemos microcomputers and developed little devices for environmental monitoring (climate and volatile organic compounds, VOCs). During this year, I advanced quickly, from first (very ugly) experimental circuits to professional PCBs with Internet-of-Things capability. This project is now running on its own, and we will continue to develop the MeteoMex platform as a community kit.

Although our primary interest is academic and not a business, I can see significant progress in the consolidation of our company.

What happened to my laboratory in Mexico?

I have to admit that I felt somehow guilty to leave my research group labABI on its own for one year. Of course, we kept in contact by email and weekly reports (;-)), but the daily communication and coffee were missing. My colleague Alejandro Blanco (Many thanks!!) supervised the group during this time and supported us in case of administrative tasks and problems. During my absence, one last-year Ph.D. student left the lab to become a solopreneur in organic foods. Although this is a pity for the postgraduate program, he looks happy when I meet him at the institute or in the city. Two PhDs and one M.Sc. student of the labABI graduated shortly after my return and found jobs. In all aspects, the productivity of the laboratory was higher than in years with my physical presence.

Impact on physical and mental health

Despite a typical Bavarian/ German "diet" during the sabbatical, my metabolic status (cholesterol, triglycerides, etc.) improved significantly, which indicates that stress indeed affects your (objectively measurable) health. I recognized that nothing critical happens if I am not always available. Now, I just hope to keep that in mind for avoiding future self-exploitation.

Coming home and being 'guest.'

If you return after more than ten years living abroad to your homeland, this situation is kind of weird. Maybe comparable to returning to your parents' house after a long absence. You know all the furniture and the taste of the food, but anyhow you feel more like a guest than really belonging there.

It is never valid to compare two countries, but I could compare Germany when we left it in 2008 and today. To my impression, the social system and public services, such as the train system, notably reduced their quality. The country, which is based on technology and knowledge, lost leadership in comparison to other countries such as China. In science, we can see the rise of China very clearly and taking away an editorial bias; the picture would be even more drastic. Europe and the US are becoming less important in the future world, and maybe it's time to recognize that fact.

This is not a political blog, but I hope that global development will go towards collaboration and social and economic fairness. Anyhow, I think it would be a pleasant experience for political leaders to live other realities, such as other countries or social environments—for example, a sabbatical as an unemployed or migrant. Only changing the perspective can reveal new insights.

Résumé

The sabbatical year was rich in experiences and more fertile than just another 'routine' year.

Even if you consider yourself indispensable at work, you should do it!


γνῶθι σεαυτόν (know thyself)

Citation reports and lab presentations are the daily bread of a scientist. To make life a little less painful, I wrote an R markdown script that pulls my bibliographic data from the ORCID and Crossref databases, and creates a word cloud and two tabular reports. The R markdown script runs in RStudio. For my ORCID identifier ('0000-0001-6732-1958') the word cloud presented in the blog article graphics is produced. This image is exported to a png file. The citation summary, based on Crossref data, gives realistic data (a bit lower than Google Scholar, and similar to ISI Web of Knowledge analyses):

  publications sum_citations H_factor
Winkler, Robert 82 1439 21

Co-authors are sorted, according to the number of co-authored papers:

  orcid_ident orcid_coauthor_names coauthor_freq
1 0000-0002-0367-337X Hertweck, Christian 12
2 0000-0001-8228-7663 Moreno-Pedraza, Abigail 8
3 0000-0002-4908-8934 Martínez-Jarquín, Sandra 7
4 0000-0001-8041-8586 Gamboa Becerra, Roberto 5
5 0000-0002-3463-957X García-Lara, Silverio 5
6 0000-0002-7471-9152 Montero-Vargas, Josaphat Miguel 5
7 0000-0002-9493-6402 Kniemeyer, Olaf 5
8 0000-0001-7738-7184 Ordaz-Ortiz, Jose Juan 4
9 0000-0002-6738-9554 López-Castillo, Laura Margarita 4
10 0000-0002-2097-0464 De Vizcaya-Ruiz, Andrea 3
11 0000-0003-0973-9728 Escamilla-Rivera, Vicente 3
12 0000-0001-6230-8092 Délano-Frier, John Paul 2
13 0000-0001-7827-486X Barraza, Aarón 2
14 0000-0001-8037-2856 Partida-Martinez, Laila P. 2
15 0000-0001-8080-5797 Garcia-Cuellar, Claudia Maria 2
16 0000-0002-3600-050X Alvarez-Venegas, Raúl 2
17 0000-0002-4589-6870 Herrera-Estrella, Alfredo 2
18 0000-0002-6028-0425 Hube, Bernhard 2
19 0000-0002-7397-2092 Vergara, Fredd 2
20 0000-0002-8982-5070 Jimenez-Sandoval, Pedro 2
21 0000-0003-1689-7759 Ramirez-Chavez, Enrique 2
22 0000-0003-2371-0307 Molina Torres, Jorge 2
23 0000-0003-4363-7274 de Folter, Stefan 2
24 0000-0001-6203-0342 Ortiz-Martinez, Margarita 1
25 0000-0001-6668-217X Tefsen, Boris 1
26 0000-0001-7096-2713 Garza-Rodríguez, Maria Lourdes 1
27 0000-0001-7700-039X Richter, Ingrid 1
28 0000-0001-8001-6843 Itouga, Misao 1
29 0000-0001-8032-9890 Treutler, Hendrik 1
30 0000-0001-8561-7170 Pedruzzi, Ivo 1
31 0000-0001-9224-0455 Rodríguez-López, Carlos 1
32 0000-0001-9489-2545 Villegas-Sepulveda, Nicolas 1
33 0000-0001-9503-9634 Heinekamp, Thorsten 1
34 0000-0001-9522-0062 Marsch Martinez, Nayelli 1
35 0000-0001-9671-0784 Guntinas-Lichius, Orlando 1
36 0000-0001-9702-9480 Heim, Joel Benjamin 1
37 0000-0002-0309-604X Capella-Gutierrez, Salvador 1
38 0000-0002-0368-6007 Urrea-López, Rafael 1
39 0000-0002-0584-2093 Telle, Sabine 1
40 0000-0002-1056-4665 Gepts, Paul 1
41 0000-0002-1977-0115 Rodríguez Sixtos Higuera, Alicia 1
42 0000-0002-2826-2518 Mayolo-Deloisa, Karla 1
43 0000-0002-2943-7754 Valdés-Santiago, Laura 1
44 0000-0002-3789-1826 Vizuet-de-Rueda, juan carlos 1
45 0000-0002-4187-2863 Feuermann, Marc 1
46 0000-0002-4241-2674 Vlasova, Anna 1
47 0000-0002-4459-9727 Braun, Hans-Peter 1
48 0000-0002-4509-7964 Abud-Archila, Miguel 1
49 0000-0002-5321-1763 Rito-Palomares, Marco 1
50 0000-0002-5408-4022 Herrera-Ubaldo, Humberto 1
51 0000-0002-6392-170X Azuara-Liceaga, Elisa 1
52 0000-0002-7472-9844 Trevino, Victor 1
53 0000-0002-7727-6967 Rosas Román, Ignacio Raúl 1
54 0000-0002-8062-6999 von Eggeling, Ferdinand 1
55 0000-0002-8132-8651 Brunkhorst, Frank Martin 1
56 0000-0002-8442-514X González-González, Mirna 1
57 0000-0002-9061-1061 Glöckner, Gernot 1
58 0000-0002-9455-0796 Krewinkel, Albert 1
59 0000-0002-9751-6702 Shelest, Ekaterina 1
60 0000-0003-1361-5162 Tamez-Pena, Jose 1
61 0000-0003-1679-3247 Doyle, Sean 1
62 0000-0003-1939-9181 Diaz Flores, Maria Fernanda 1
63 0000-0003-1948-3391 Werner, Ernst R. 1
64 0000-0003-2469-3238 Ayora-Talavera, Teresa del Rosario 1
65 0000-0003-3156-5779 Lozano Garcia, Omar 1
66 0000-0003-3186-0292 Kavanagh, Kevin 1
67 0000-0003-3229-1378 White, Theodore 1
68 0000-0003-3888-0931 Weiskirchen, Ralf 1
69 0000-0003-4163-7334 Imhof, Diana 1
70 0000-0003-4193-2720 Delaye, Luis 1
71 0000-0003-4322-0145 Santos, Herbert 1
72 0000-0003-4494-1446 Mejía-Giraldo, Juan Camilo 1
73 0000-0003-4839-3117 Deufel, Thomas 1

These tables are saved in CSV format and can be easily imported into spreadsheet programs (e.g. LibreOffice or Microsoft EXCEL) for producing charts. The R markdown script can be downloaded from GitHub.

As you may notice, the supervisor of my PhD and PostDoc time still occupies the first place of co-authors, which demonstrates that my time in the Hertweck lab was really productive. The following ranks are very successful M.Sc. and PhD students that worked in my lab, as well as my best internal and external collaborators. Listing the publications with internal co-authors demonstrates the vital role of my lab for the institution. Besides, this list helps me to spot productive collaborators for fund proposals and future research projects. You always should bet on the fastest horse and the winning team!

Word cloud and bibliographic analyses are based on your global output. However, they might reflect, how other researchers might perceive your work. But you also can modify the R script and search by intervals. For example, to compare the most frequent article title words during your PhD time and after getting an independent position as a group leader.

Observing the development of your research focus during your academic life can be an extraordinary experience; give it a try!


Colemak: The ideal keyboard layout for multilingual scientists

As scientists, we frequently need special symbols such as ±, ‰, µ. Many researchers also have to write in multiple languages. As a Bavarian/German that works in Mexico and publishes principally in English, I switch continuously between typing in German, Spanish and English, meaning that I need letters on the keyboard that are typical for those languages, such as ñ, é, ü, ß etc. As you might know, dealing with a considerable variety of symbols on a standard keyboard layout is tricky. In contrast, the Colemak keyboard layout provides shortcuts for commonly used letters in the Latin writing system.
But the real reason, why I changed to the Colemak keyboard layout, was a different one: at a very vivid conference dinner of the Mexican Society of Biochemistry, I cut a tendon of my left index finger. As a consequence, I required two surgeries and more than 100 sessions of physiotherapy. Nevertheless, a complete recovery of the functionality was not possible. Prolonged typing was painful, and therefore I looked for solutions. The first steps were a competent dictation software (Swype and Dragon) and a mechanical keyboard (Corsair Strafe with blue Cherry switches). Dictation of e-mails and typing with a high-quality keyboard was already a significant improvement toward ergonomic writing. But still, I had to move my stiff finger for every 't', motivating me to try alternative keyboard layouts. Finally, I discovered the Colemak layout, which is designed for optimizing the finger movements and for multilingual writing. Compared to other ergonomic arrangements such as DVORAK, fewer keys are different, which facilitates the learning. The Colemak webpage provides training strategies and software recommendations.
Sometimes you want to cheat and see the keys (e.g. for typing your complicated password)? In this case, you either can define a key for switching keyboard layouts (I am using the [Win] key to change between Colemak and US layout). Or, you re-label the keyboard with stickers. Thanks a lot to Roman Glinnik, who created high-quality labels for Colemak!
Of course, switching to a new keyboard layout reduces your typing speed for several days or weeks. But in the long term, you write faster and reduce your risk of repetitive strain injury (RSI).

Use artificial intelligence!

Search engines, shopping platforms and social media networks make great use of algorithms for identifying patterns in massive data sets, and help us to find relevant information, products and friends. In stark contrast, many scientists 'do not trust' artificial intelligence. Of course, hypothesis-driven research, according to Popper's Scientific Method (Popper, Karl R. 1959. The Logic of Scientific Discovery. Oxford, UK: Basic Books.), is still the gold standard. But how should we deal with data from exploratory projects such as genomics, proteomics, metabolomics, etc.?
Data Mining methods combine general statistics with machine learning and help us to detect important variables and associations. Further, we can build predictive models for classification or quantification. For mass spectrometry data sets, we found notably the Random Forest Tree algorithm useful since it performs well with noisy data and relatively few samples. Thus, next time you analyse a few thousand variables from a dozen samples, you should try Rattle, free Data Mining software available from https://rattle.togaware.com/. This R package implements various algorithms such as Decision Tree, Random Forest Tree, Ada Boost, Support Vector Machine and Neuronal Networks. The Graphical User Interface of Rattle is human-friendly and also suitable for beginners (BTW: Graham Williams, the author of Rattle, works at the Australian Taxation Office).
Soon (~March 2020) we will publish our RSC book "Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide" (http://pubs.rsc.org/bookshop/collections/series?issn=2045-7545). The co-authors Miguel Reboiro-Jato, Daniel Glez-­Peña and Hugo López-­Fernández contributed a chapter about "Statistics, Data Mining and Modeling", demonstrating with code examples various advanced strategies for data processing, such as self-organising maps (artificial neural networks), biomarker discovery and predictive machine learning models.
Thus, enter the next level of Omics data analysis and use artificial intelligence!

Academic writing: docx, LaTeX or markdown?

Today I wrote my productivity report for 2019. Of course, I was using the official .doc (!) format of our institution. As well, I wrote four letters with my .docx and .odt templates. Word (https://products.office.com/word), LibreOffice (https://www.libreoffice.org/) and similar "What You See Is What You Get" (WYSIWYG) word processors are ideal for quickly creating simple documents.
However, for scientific manuscripts or dissertations, you can use more advanced programs. The reference for academic typesetting is LaTeX (https://www.latex-project.org/). Writing a text is somehow similar to programming, and the produced PDF files are ready to publish. However, little errors, such as a forgotten '}' may cause hours of bug hunting and drive away beginners. Online services, such as Overleaf (https://www.overleaf.com/) greatly facilitate the use of LaTeX and collaborative working. LaTeX is the first choice for people who aim towards correctly set equations and beautiful outcomes.
In the last years, writing texts in markdown is becoming increasingly popular. The plain text files contain only a few special commands that define the structure, such as '#' for a section heading, or formatting, such as '**' for bold text. Thus, the syntax is easy to learn, and the files can be opened with any text editor. There are exclusive markdown "What You See Is What You Mean" (WYSIWYM) editors such as Ghostwriter (https://wereturtle.github.io/ghostwriter/), but also working with more nerdy editors such as Atom (https://atom.io/) or Vim (https://www.vim.org/) is possible. Several programs already provide exporting the markdown text to docx, odt, html or pdf. Pandoc (https://pandoc.org/) enables the use of custom templates, e.g. the latex or docx style templates of journals. Markdown files are very light-weight, cross-platform compatible and mobile-friendly.
If you are interested and look for more information:
Krewinkel A, Winkler R. 2017. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. PeerJ Computer Science 3:e112, https://doi.org/10.7717/peerj-cs.112

(Bio)chemistry is not sexy

This is quite clear to me. Although I try to convince students, colleagues and executives that molecules are the basis of life, since they provide energy (ATP), store information (DNA), enable movement (actin), kill enemies (chloramphenicol), control libido (testosterone; see fig.), etc., they seem to be boring, and knowledge about (bio)chemistry irrelevant. Yes, teaching can be quite frustrating...

Currently, a lot of resources are spent in sequencing genomes of microbes, animals and plants. But is this useful if we do not study their metabolic activity at the same time? I have not seen many success stories of eradicating diseases or improving crops from genomics. We will have to fill the genomes with life.

Be prepared:
The era of (bio)chemistry is just coming!

I am a Scientist; why should I blog?

I got a position as a principal investigator, and my 1-page contact gets renovated automatically as long as I work and avoid stupid mistakes.
My lab is publishing, and my graduate students usually quickly find good jobs.
My research funding is limited (did I mention that my lab is located in Irapuato, Mexico?), but the salaries of all lab members are safe.

So, why should I bother myself with writing a Blog?

A Blog will neither augment my (auto)citation number, nor my income. In contrast, it will cost me time and money.

Well, there are several motivating reasons, such as:

1) (Re)connecting science and society.
Although we receive public funding, most of our results are (in the best case) only available to other researchers. "Paywalls" of scientific publishers, and complicated terminology avoid the knowledge transfer to the general public. Thus, essential findings, such as the causes of the climatic change and the distribution of microplastics in the biosphere are not used efficiently for preventing environmental catastrophes. Possibly beneficial inventions for medicine and agriculture, such as genome editing, could be ignored or rejected by the society if there is insufficient information for a constructive discussion.

2) Presenting alternative technologies.
Do-it-yourself gadgets and open-source software (OSS) packages often can replace commercial devices and software platforms. Free solutions even might offer superior features. Since non-commercial technologies usually have no marketing budget, they are less known. I want to alleviate this situation a little. Thus, if you know about any exciting innovation that could fit into the topics of the Blog, please drop me a notice.

3) Exchanging personal experiences and views.
Every person and career is different. However, I will share some conclusions from my first decade as an independent researcher, e.g. on career planning, research field definition, productive writing, funding, collaborations, and work-life balance. You might even discover that a scientist's life is not for you...

Naturally, any information posted on this Blog is biased by my personal opinion and philosophy. Nevertheless, if you like my Blog, you can follow it; comment, suggest or contribute articles.

Robert Winkler

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