From: Paul Ryan Sent: 28 September 2016 12:47 To: O'Toole, Paul; CORA Institutional Repository Subject: RE: PhD Hi Gillian, Apologies, I had misread the email sender and thought that Prof. O' Toole was saying that he was happy for it to appear online - but he is right, it is long and contains too much information. Please keep it offline. Many thanks, Paul From: O'Toole, Paul [pwotoole@ucc.ie] Sent: Wednesday, September 28, 2016 12:44 PM To: CORA Institutional Repository; Paul Ryan Subject: Re: PhD no dont Gillian; I have explained to Paul that it is very long and discloses a lot and could compromise IP. Paul W. O'Toole Ph.D., Prof. Microbial Genomics School of Microbiology & APC Microbiome Institute Room 447 Food Science Building, University College Cork, T12 Y337 Cork, Ireland. Tel: 353 21 490 3997 pwotoole@ucc.ie http://apc.ucc.ie/ http://www.researcherid.com/rid/G-1593-2012 Senior Editor, Microbiology http://mic.sgmjournals.org/ From: CORA Institutional Repository Sent: 28 September 2016 12:41 To: Paul Ryan; CORA Institutional Repository; O'Toole, Paul Subject: RE: PhD Thanks Paul, I’ll put it up. Regards, Gillian From: Paul Ryan [mailto:Paul.Ryan@teagasc.ie] Sent: 28 September 2016 12:40 To: CORA Institutional Repository ; O'Toole, Paul Subject: RE: PhD Hi Paul, I'm happy for the abstract to appear online in Cora. Thanks, Paul From: CORA Institutional Repository [cora@ucc.ie] Sent: Wednesday, September 28, 2016 9:13 AM To: O'Toole, Paul Cc: Paul Ryan Subject: FW: PhD Hi Paul, Just checking again whether we can upload the Abstract of this thesis to CORA or if you’d prefer to leave it out? Thanks, Gillian Gillian Cotter | Library Assistant, Institutional Repository |Boole Library, University College Cork, Ireland + 353 (0) 21 420 2284 |g.cotter@ucc.ie , cora@ucc.ie | Cork Open Research Archive http://cora.ucc.ie/ University College Cork is named The Sunday Times University of the Year 2016: www.ucc.ie/en/ From: Herlihy, Breeda On Behalf Of CORA Institutional Repository Sent: 16 September 2016 14:39 To: O'Toole, Paul ; Paul Ryan ; Catherine Stanton ; pxr999@gmail.com Cc: Curran, Brendan ; CORA Institutional Repository Subject: RE: PhD Dear all, Thanks all for the clarification. We will leave the 5 year embargo on the hard bound thesis. No e- thesis was submitted to CORA so there is nothing to embargo. Very occasionally we are asked to embargo an abstract. Is this required in this case? Best regards, Breeda Breeda Herlihy | Manager - Institutional Repository | Research and Digital Services | Boole Library | University College Cork, Ireland + 353 (0) 21 420 5109 | b.herlihy@ucc.ie , cora@ucc.ie | Cork Open Research Archive http://cora.ucc.ie/ University College Cork is named The Sunday Times University of the Year 2016: www.ucc.ie/en/ From: O'Toole, Paul Sent: 16 September 2016 14:24 To: Paul Ryan; Catherine Stanton; pxr999@gmail.com Cc: Curran, Brendan; CORA Institutional Repository Subject: RE: PhD That is great thanks Paul, if you already requested a 5 year embargo, that is ample. Paul O’Toole. Paul W. O'Toole Ph.D., Prof. Microbial Genomics School of Microbiology & APC Microbiome Institute Room 447 Food Science Building, University College Cork, T12 YN60 Cork, Ireland. Tel: 353 21 490 3997 pwotoole@ucc.ie http://apc.ucc.ie/ http://www.researcherid.com/rid/G-1593-2012 Senior Editor, Microbiology http://mic.sgmjournals.org/ From: Paul Ryan [mailto:Paul.Ryan@teagasc.ie] Sent: Friday 16 September 2016 12:40 To: O'Toole, Paul ; Catherine Stanton ; pxr999@gmail.com Subject: RE: PhD Dear Paul, In fact I am registered for Cora on my Teagasc email (paul.ryan@teagasc.ie) and I submitted an abstract, as is required to submit the hardbound thesis, but I had requested a 5-year embargo on both the electronic thesis and hardbound thesis. However, if it is preferable to make this indefinite then I am happy with that also. So we can invoke option two. Many thanks, Paul From: O'Toole, Paul [pwotoole@ucc.ie] Sent: Friday, September 16, 2016 12:20 PM To: Catherine Stanton; Paul Ryan; pxr999@gmail.com Subject: FW: PhD Dear Paul, can you review this thread please and come back to us on which option we can invoke? Thanks Paul. Paul W. O'Toole Ph.D., Prof. Microbial Genomics School of Microbiology & APC Microbiome Institute Room 447 Food Science Building, University College Cork, T12 YN60 Cork, Ireland. Tel: 353 21 490 3997 pwotoole@ucc.ie http://apc.ucc.ie/ http://www.researcherid.com/rid/G-1593-2012 Senior Editor, Microbiology http://mic.sgmjournals.org/ From: Herlihy, Breeda On Behalf Of CORA Institutional Repository Sent: Friday 16 September 2016 11:43 To: Buckley, Helen ; CORA Institutional Repository Cc: O'Toole, Paul Subject: RE: PhD Dear Paul, An embargo is requested by the student when they make their submission to CORA. I have checked the e-mail address of the student 108444161@umail.ucc.ie and pxr999@gmail.com but he doesn’t seem to have registered with CORA. Could you send me his full name? As it seems the student has not yet uploaded anything to CORA, he has two options 1. Upload thesis abstract to CORA, indicate an opt out of e-thesis submission and set an indefinite embargo request on the hard bound thesis. Complete the attached form and return to the Graduate Studies Office. 2. Upload thesis abstract and e-thesis to CORA, set an indefinite embargo request on the hard bound thesis and e-thesis. Best regards, Breeda Breeda Herlihy | Manager - Institutional Repository | Research and Digital Services | Boole Library | University College Cork, Ireland + 353 (0) 21 420 5109 | b.herlihy@ucc.ie , cora@ucc.ie | Cork Open Research Archive http://cora.ucc.ie/ University College Cork is named The Sunday Times University of the Year 2016: www.ucc.ie/en/ From: Buckley, Helen Sent: 16 September 2016 11:14 To: CORA Institutional Repository Cc: O'Toole, Paul Subject: FW: PhD From: O'Toole, Paul Sent: 16 September 2016 10:41 To: Buckley, Helen Cc: Catherine Stanton; Paul Ryan; pxr999@gmail.com Subject: Re: PhD Dear Helen, In accordance with our duty of stewardship of publicly-funded Intellectual Property, we commissioned a review of this thesis and it was decided by APC Institute management to request this thesis be put under embargo. Both supervisors are in agreement. Can you tell me how to implement this? Many thanks, Paul O'Toole ------ Paul W. O'Toole Ph.D., Prof. Microbial Genomics School of Microbiology & APC Microbiome Institute University College Cork, Ireland. Tel: 353 21 490 3997 pwotoole@ucc.ie http://apc.ucc.ie http://www.researcherid.com/rid/G-1593-2012 Senior Editor, Microbiology: http://mic.microbiologyresearch.org/content/journal/micro On 14 Sep 2016, at 16:47, Buckley, Helen wrote: Dear Paul I acknowledge safe receipt of your hardbound thesis. I can also confirm that ACGSC approved the examiners report for your examination. To be conferred with your doctorate at the Autumn Conferring Ceremony (17-28 October 2016), the following must be done by 5.00pm 15th September 2016: i) Submit a letter from your Internal Examiner confirming that the corrections have been made or an email sent by your Internal Examiner to h.buckley@ucc.ie confirming that the amendments have been carried out. Kind regards Helen From: Buckley, Helen Sent: 02 September 2016 15:25 To: '108444161@umail.ucc.ie'; 'pxr999@gmail.com' Cc: O'Toole, Paul; 'catherine.stanton@teagasc.ie'; Fitzgerald, Gerald; Ross, Paul; Dinan, Ted; Microbiology Secretary Subject: PhD Dear Paul I can confirm that I have received the examiner’s report for your PhD examination. The report will be considered at Academic Council Graduate Studies Committee on September 14th. In the meantime, to be conferred with your doctorate at the Autumn Conferring Ceremony (17- 28 October 2016), the following must be done by 5.00pm 15th September 2016: Step 1 - Electronic Submission i) Submit your abstract (not exceeding 300 words) on-line through CORA, the UCC institutional repository http://cora.ucc.ie. To submit on-line, you must first register with CORA at https://cora.ucc.ie/register and then complete a thesis description form and upload your thesis abstract (not exceeding 300 words). Please note registration with CORA can take up to three working days. ii) If you are submitting an e-thesis you can also do this through CORA. iii) If you are not submitting an e-thesis, you must complete a ‘Decision to withhold form’ with your supervisor and submit this to the Graduate Studies Office. This form is also available from the Graduate Studies Office & Boole Library websites -- http://booleweb.ucc.ie/documents/Decision_to_Withold.pdf Step 2 – To the Graduate Studies Office i) Submit one hardbound copy of your corrected thesis to the Graduate Studies Office (hardbound thesis can be printed double sided). ii) Submit a letter from your Internal Examiner confirming that the corrections have been made or an email sent by your Internal Examiner to h.buckley@ucc.ie confirming that the amendments have been carried out. iii) Hardbound thesis submission form (attached) iv) If not submitting ethesis, Decision to withhold form (if seeking to withhold) http://booleweb.ucc.ie/documents/Decision_to_Withold.pdf Please note that you don't have to submit in person, someone else can submit on your behalf or you can submit by post. The office is opened Monday to Friday from 9.00am – 1.00pm and 2.00pm – 5.00pm. Training guides on how to upload to CORA are available from http://booleweb.ucc.ie/index.php?pageID=503/ Frequently asked questions on e-theses are available from http://booleweb.ucc.ie/index.php?pageID=506 Information on thesis submission procedures is available from the Graduate Studies Office http://www.ucc.ie/en/graduatestudies/current/thesis/s_phd_thesis/ Binding of Hardbound Thesis: A list of binding companies is available on our website at http://www.ucc.ie/en/graduatestudies/thesis/. The final copy of the thesis must be a hard bound copy -- the thesis shall be bound within boards and cannot have metal spines glued to the front and back covers. The cover colour is up to the candidate. The binding shall be of a fixed kind in which leaves are permanently secured. The boards shall have sufficient rigidity to support the weight of the work standing upon a shelf. Front Cover: 1/4 way down - Full Title of Thesis; 1/2 way down - Full Name Spine: Left Hand Side - Degree (e.g. PhD) Middle – Name (your full name) Right Hand Side - Year (i.e. 2016) Conferring Ceremonies: Once you are eligible to graduate, the Office of Marketing & Communications will send a conferring information pack by post to your student college-registered address one week prior to the ceremony. Your college-registered home address is on your student portal. Please ensure this address is accurate four weeks in advance of your conferring date. If you need to update it after this date, please let the Office of Marketing & Communications know by emailing conferrings@ucc.ie. Should there be any updates on the conferrings, please note that information will be sent to you student email account (i.e. ...@umail.ucc.ie). Schedule: Once the schedules of conferring ceremonies have been prepared, they will be available to view here; http://www.ucc.ie/en/conferrings/ Frequently Asked Questions: If you would like to check a list of frequently asked questions (FAQ’s) in relation to UCC’s conferring ceremonies, please visit; http://www.ucc.ie/en/conferrings/theday/ Queries about the Conferring Ceremonies: If you have a specific query in relation to UCC’s conferring ceremonies, please contact: Office of Marketing & Communications at Tel: +353 (0)21 490 2202 , Email: conferrings@ucc.ie, website http://www.ucc.ie/en/conferrings/. Non-EU Students - Visa Certification Letter of Invitation to Conferring Ceremonies: Should you require a letter of invitation for visa purposes, you should call to Student Records and Examinations, 1st Floor West Wing, UCC (Email: exams@ucc.ie) and bring with you the following: i) Your student ID card and ii) A copy of this email or your result letter that has been posted to you. Third Level Graduate Scheme: International students are entitled to remain for up to 12 months in Ireland after receiving their exam results under the Third Level Graduate Scheme, for the purposes of seeking employment and applying for a green card or work permit. For more information on this, please visit http://www.icosirl.ie/eng/student_information/third_level_graduate_scheme and http://www.inis.gov.ie/en/INIS/Pages/WP11000076. Transcript If you require a transcript, you can order from Student Records and Examinations at exams@ucc.ie. Spread the word about your research Congratulations on finishing your doctorate at UCC. UCC has a new blog and we would love it if you would contribute and spread the word about your research. UCC has an abundance of interesting, exciting and unusual research projects and we’d like to share these stories. We are now using the new blog to showcase UCC research to a wide audience. Your posts will be live on our blog and the blog will be shared on all UCC social media networks. We are seeking 200- 500 words and a photograph to accompany the online piece. Please contact Carol Veiga, EU Postgraduate Officer (carol.veiga@ucc.ie) for more details. Get inspired by this great research site from University of Southampton. Please help us turn your research into a consumable story that we can help share. Kind regards Helen Helen Buckley | Research Student Administrator | Graduate Studies Office | 2nd Floor West Wing | University College Cork | Cork | Ireland | Tel: + 353 21 4205198 | Email: h.buckley@ucc.ie University College Cork is named The Sunday Times University of the Year 2016: www.ucc.ie/en/ Thesis Submission: http://www.ucc.ie/en/graduatestudies/thesis/ Office Opening Hours: Monday – Friday, 9.00am – 5.00pm. Attention: This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content. Tabhair aire: Tá an r-phost seo faoi phribhléid agus faoi rún. Mura tusa an duine a bhí beartaithe leis an teachtaireacht seo a fháil, scrios é le do thoil agus cuir an seoltóir ar an eolas. Is leis an údar amháin aon dearcaí nó tuairimí a léirítear. Scanadh an r-phost seo le Teagasc agus deimhníodh go raibh sé saor ó víoras leis an bpatrúnchomhad atá in úsáid faoi láthair. Ní féidir a ráthú leis seo áfach nach bhfuil ábhar mailíseach ann. Attention: This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content. Tabhair aire: Tá an r-phost seo faoi phribhléid agus faoi rún. Mura tusa an duine a bhí beartaithe leis an teachtaireacht seo a fháil, scrios é le do thoil agus cuir an seoltóir ar an eolas. Is leis an údar amháin aon dearcaí nó tuairimí a léirítear. Scanadh an r-phost seo le Teagasc agus deimhníodh go raibh sé saor ó víoras leis an bpatrúnchomhad atá in úsáid faoi láthair. Ní féidir a ráthú leis seo áfach nach bhfuil ábhar mailíseach ann. Attention: This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content. Tabhair aire: Tá an r-phost seo faoi phribhléid agus faoi rún. Mura tusa an duine a bhí beartaithe leis an teachtaireacht seo a fháil, scrios é le do thoil agus cuir an seoltóir ar an eolas. Is leis an údar amháin aon dearcaí nó tuairimí a léirítear. Scanadh an r-phost seo le Teagasc agus deimhníodh go raibh sé saor ó víoras leis an bpatrúnchomhad atá in úsáid faoi láthair. Ní féidir a ráthú leis seo áfach nach bhfuil ábhar mailíseach ann.