Manuscript self-archiving #1: many questions!

Hello all!

If you have read the Preprint , you know that I am trying to act and become 100% open access with my manuscripts. I made a list of the publications with links to the PDFs available online without a paywall (if the paper is open access or available in other websites) but there are still a few publications that require a subscription to the journal.

I thought it would be interesting to write about my “becoming open access” process as it seems that it will be tricky (but I am sure feasible) for a few reasons:

1-  Which version of the manuscript is acceptable to make a preprint of when the manuscript has already been published?

  • Should I use the first submission version (but sometimes major changes have been done before the second submission)?
  • Can I make a preprint of the resubmission (without the publisher’s proofreading)?
  • Or can I make a preprint of the last version of the manuscript before they prepared the layout?

2- Are there any publishers that do not allow at all to have a preprint version of my work after I published it?

For instance, what does that mean??

Screen Shot 2018-01-19 at 14.41.19.png

Please don’t judge me for signing things I don’t understand, I was a naive Ph.D. student that wanted to have a publication (Okay you can judge me….)

HELP!

images

Advertisements

New research life in Edinburgh: fieldwork in California, blogging about nature crazy sex life and more

2017-04-11 11.54.31
Vine mealybugs in North California vineyard

Hello everyone,

A lot has happened since I moved to Edinburgh. Here are the main updates:

  • I am currently carrying out fieldwork in California until May, and looking for obscure mealybugs with B chromosomes. Follow me on Twitter!
  • In August, you will see me at ESEB2017 in Groningen, where I will present my work on scale insect adult metamorphosis.

Why should biologists use GitHub?

Screen Shot 2016-05-08 at 3.45.28 PM
from GitHub repository here

Today, all biologists use computers on a daily basis, produce and analyse data. A lot of us now have to learn programming (even just some bits of it).

I am not a computer scientist/engineer, and I am far from a bioinformatics person (yet), but I have started to discipline myself to make my published research as reproducible as possible and this is not only by depositing DNA sequence data to NCBI, but also analysis pipelines and command lines made available to the public on GitHub.

GitHub is a great public repository hosting service for publishing programming source code, but it can also be used to detail your analysis pipeline and code, and even create tutorials on softwares or pipelines for others.

For example, the Trinity tutorial from Brian Haas was a life saver for a biologist like me that had never touched any next-generation sequencing data.

As a biologist, to support my recent publication on scale insect phylogenetics, I created a GitHub repository that details all the steps and command lines in MrBayes and R analyses. This provides transparency to the reader and more rapid reproducibility.

Tip: If you are worried about your analysis pipeline or data being online during the manuscript review process, academic researchers can apply for free space for 5 private repositories. For more information, check here.

Nowadays, a lot of biologists will come to work in a multidisciplinary environment, and it implies learning new skills. In bioinformatics in particular, workshops are available but the internet is a great resource to learn skills by ourselves and GitHub can help both learning how a software works, but also making the details of informatics methods available to other biologists that are also learning how to use these softwares (from command lines for de novo assembly using Trinity or making a simple plot with R).

 

 

SICB2016: Society for Integrative and Comparative Biology meeting

Kicking off 2016 with the SICB annual meeting which is taking place in Portland and starting on January 3rd.

I will be presenting poster and oral presentations related to my postdoctoral work on the hormonal regulation of extreme sexual dimorphism in scale insects.

This is my first SICB meeting and I am excited to meet people working on other taxonomic groups than insects!

Follow #SICB2016 on Twitter for live updated of the meeting.

10th International Conference on Juvenile Hormone

The 10th International Conference on Juvenile Hormone will be held at Tsukuba (not far from Tokyo) between June 9th and 13th.

This conference takes place every four years or so. The last one was in 2007 though, and this one was supposed to happen in 2011 in Japan but was cancelled because of the earthquake (Dr Minakuchi, pers. com.).

This will be my first conference outside the field of systematics/phylogeny/scale insects, in which I will present our preliminary results on scale insect sexual dimorphism linked with Juvenile Hormone.

Five big names in the field of JH will give plenary lectures: Xavier Belles, Marek Jindra, Reddy Palli, Alexander Raikhel and Lynn Riddiford.

Additionally, there are some exciting talks I am looking forward to, such as the action of JH in insect embryos (J.W. Truman), JH and aphid polyphenism (T. Miura)  etc.. There seems to have quite a diverse range of study organisms as well, which is exciting!

For a glance at next week program -> here

The giant scale Drosicha corpulenta: on uncovering its biology

Photo credit: Isabelle Vea
Photo credit: Isabelle Vea

May 4, 2014

Walking back from lunch and discussing with my boyfriend and a friend visiting from Kobe, I was looking down and spotted a large bug crawling on the ground. I first thought it was a pill bug with a very strange color, but half a second later, I kneeled and realized it was a giant scale insect, Drosicha corpulenta! What a sight, I have never seen this genus alive and was elated to be able to observe them walking. They were many on the ground, probably because it was very windy. We collected a couple of them.

May 7, 2014

Morning: I tried to look for the tree where they were feeding and found a few different tree species infested. I could not find any males.

After lunch: Next to my lab, I noticed a group of trees, and immediately was shocked to see the large infestation of the same scale insects. I pass by this group of trees everyday since I arrived in Nagoya University, how come I haven’t seen them before? Immediately, I try to evaluate the extant of the infestation. They are almost on every single tree. Trying to look for a male, I finally find one hanging on a tree trunk. End of afternoon: I go back to look for more males. I will find a total of 4 in the following days.

I kept a dozen females and the 4 males in a box for a few days. This video shows a male walking on a female.

The males died after 3-4 days of frantic copulation.

Photo of a male, dropping dead after his last female encounter. The endophallus (= penis) is out. This is the first time I see a scale insect penis (I have only seen slide preparations and fossilized ones). In a few scale insect families, the endophallus looks like this, and can be longer, with many spikes covering it. Other families such as the soft scales or mealybugs don’t have an endophallus. Notebook 4-8 May 10, 2014

With a colleague we bought a persimmon tree so we could collect and observe some females. Drosicha corpulenta feeds on many species and is considered a plant pest in Japan. Here is the list of plant species they have been found feeding on.

May 11, 2014

I collected a few females and put them in the soil of our persimmon tree. Half an hour later, I checked the tree and a few of them had climbed up the branches and settled to feed.

May 12, 2014

I checked the persimmon tree and the females are still feeding.

May 15, 2014

I went back to the infestation spot to collect some more individual for the persimmon tree. Most of the females are GONE. Where they were gathering by dozens, nothing is left. I was puzzled at first. What did happen? I thought that the gardeners of the university wiped out the branches of all trees, but this would be unlikely as even the oak higher branches don’t have scale insects anymore. Also, the branches really looked clean. So my alternative hypothesis is that the females marched down to the ground to lay eggs at the same time! Alternatively, on my persimmon tree, the females that were feeding on May 12 are also gone. I need to look at the soil and check my theory. According to Scalenet, the reference database for scale insects, there is an account on their biology in:

Kuwana, S.I. 1922. Studies on Japanese Monophlebinae. Contribution I: The genus WarajicoccusBulletin of Agriculture and Commerce, Imperial Plant Quarantine Station, Yokohama 1: 1-58. 

I went to the agriculture library of my building and could only find Contribution II of the journal…

May 20, 2014

The university  library managed to find a copy of the publication! This study from 1922 provides a biological account of the genus Drosicha (then Warajicoccus) additionally to morphological descriptions of all stages (juveniles, female and male). Beautiful hand drawn plates are also presented at the end of the booklet. Kuwana confirms that when the adult females are ready to lay eggs, they migrate to the ground and hide among tree leaves and other litter matter.

To be continued….